Climate Change and Crop Production

CABI Climate Change Series

Climate change is a major environmental challenge to the world today, with significant
threats to ecosystems, food security, water resources and economic stability overall. In order
to understand and research ways to alleviate the effects of climate change, scientists need
access to information that not only provides an overview of and background to the field, but
also keeps them up to date with the latest research findings.
This series addresses all topics relating to climate change, including strategies to develop
sustainable systems that minimize impact on climate and/or mitigate the effects of human
activity on climate change. Coverage will therefore encompass all areas of environmental
and agricultural sciences as well as human health and tourism. Aimed at researchers, upper
level students and policy makers, titles in the series provide international coverage of topics
related to climate change, including both a synthesis of facts and discussions of future
research perspectives and possible solutions.

Titles Available
1.   Climate Change and Crop Production
Edited by Matthew P. Reynolds

Titles in Preparation
Crop Stress Management and Global Climate Change
Edited by Jose L. Araus and Gustavo A. Slafer
Cold Adaptation and Climate Change: a Mechanistic Perspective
Edited by Ken Story and Karen Tanino
Climate Change and Crop Production

Edited by

Dr Matthew P. Reynolds

International Maize and Wheat Improvement Center (CIMMYT)

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Library of Congress Cataloging-in-Publication Data

Climate change and crop production / editor, Matthew P. Reynolds
p. cm. -- (CABI series in climate change ; v. 1)
  Includes bibliographical references and index.
  ISBN 978-1-84593-633-4 (alk. paper)
  1. Crops and climate. 2. Sustainable agriculture. I. Reynolds, Matthew. P.
II. Title. III. Series.

  S600.5.C55 2010
  338.1′4--dc22
2009044409

ISBN-13: 978 1 84593 633 4

Commissioning editor: Meredith Carroll

Production editor: Tracy Head

Typeset by Columns Design Ltd, Reading.

Printed and bound in the UK by CPI Antony Rowe, Chippenham.
 Contents

Contributors vii

Foreword  x
Robert T. Watson

Preface xiv

Dedication xv

Acknowledgement xvi

Introductory Overview
1 Adapting Crops to Climate Change: a Summary 1
Matthew P. Reynolds and Rodomiro Ortiz

Predictions of Climate Change and its Impact on Crop Productivity

2 Scenarios of Climate Change Within the Context of Agriculture 9
Andy Jarvis, Julian Ramirez, Ben Anderson, Christoph Leibing and Pramod Aggarwal
3 Economic Impacts of Climate Change on Agriculture to 2030 38
David Lobell and Marshall Burke

Adapting to Biotic and Abiotic Stresses Through Crop Breeding

4 Preventing Potential Disease and Pest Epidemics Under a
Changing Climate 50
Anne Legrève and Etienne Duveiller
5 Breeding for Adaptation to Heat and Drought Stress 71
Matthew P. Reynolds, Dirk Hays and Scott Chapman
6 Breeding Crops for Tolerance to Salinity, Waterlogging and Inundation 92
Daniel J. Mullan and Edward G. Barrett-Lennard
v
CABI Climate Change Series
Climate change is a major environmental challenge to the world today, with significant
threats to ecosystems, food security, water resources and economic stability overall. In order
to understand and research ways to alleviate the effects of climate change, scientists need
access to information that not only provides an overview of and background to the field, but
also keeps them up to date with the latest research findings.
This series addresses all topics relating to climate change, including strategies to develop
sustainable systems that minimize impact on climate and/or mitigate the effects of human
activity on climate change. Coverage will therefore encompass all areas of environmental
and agricultural sciences as well as human health and tourism. Aimed at researchers, upper
level students and policy makers, titles in the series provide international coverage of topics
related to climate change, including both a synthesis of facts and discussions of future
research perspectives and possible solutions.

Titles Available
1.   Climate Change and Crop Production
Edited by Matthew P. Reynolds

Titles in Preparation
Crop Stress Management and Global Climate Change
Edited by Jose L. Araus and Gustavo A. Slafer
Cold Adaptation and Climate Change: a Mechanistic Perspective
Edited by Ken Story and Karen Tanino
vi Contents

7 Multi-location Testing as a Tool to Identify Plant Response to

Global Climate Change 115
Hans-Joachim Braun, Gary Atlin and Thomas Payne
8 Genetic Approaches to Reduce Greenhouse Gas Emissions:
Increasing Carbon Capture and Decreasing Environmental Impact 139
Martin A.J. Parry and Malcom J. Hawkesford

Sustainable and Resource-conserving Technologies for Adaptation

to and Mitigation of Climate Change
9 Greenhouse Gas Mitigation in the Main Cereal Systems: Rice,
Wheat and Maize 151
Ivan Ortiz-Monasterio, Reiner Wassmann, Bram Govaerts, Yasukazu Hosen,
Nobuko Katayanagi and Nele Verhulst
10 How Conservation Agriculture Can Contribute to Buffering
Climate Change 177
Peter R. Hobbs and Bram Govaerts
11 Management of Resident Soil Microbial Community Structure and
Function to Suppress Soilborne Disease Development 200
Mark Mazzola

New Tools for Enhancing Crop Adaptation to Climate Change

12 Biotechnology in Agriculture 219
Ryan Whitford, Michael Gilbert and Peter Langridge
13 GIS and Crop Simulation Modelling Applications in Climate
Change Research 245
David Hodson and Jeffrey White
14 Statistical Models for Studying and Understanding Genotype ×
Environment Interaction in an Era of Climate Change and
Increased Genetic Information 263
José Crossa, Juan Burgueño and Mateo Vargas

Index 285

The colour plates can be found following p. 16.

 Contributors

Dr Pramod Aggarwal, Indian Agricultural Research Institute, Environmental Sciences,

New Delhi-110012, India. E-mail: pkaggarwal.iari@gmail.com
Mr Ben Anderson, International Centre for Tropical Agriculture (CIAT), Cali, Colombia,
AA6713 and School for International Service, American University, Washington, DC
20016-8048, USA. E-mail: bowenanderson@gmail.com
Dr Gary Atlin, International Maize and Wheat Improvement Center (CIMMYT), Apdo.
Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: g.atlin@cgiar.org
Dr Edward G. Barrett-Lennard, School of Plant Biology (M084), Centre for Ecohydrology
(M084), Department of Agriculture and Food Western Australia and Future Farm
Industries Cooperative Research Centre, The University of Western Australia, 35 Stirling
Highway, Crawley, WA 6009, Australia. E-mail: egbarrettlennard@agric.wa.gov.au
Dr Hans-Joachim Braun, International Maize and Wheat Improvement Center (CIMMYT),
Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: h.j.braun@cgiar.org
Dr Juan Burgueño, Biometrics and Statistics Unit, Crop Research Informatics Lab,
International Maize and Wheat Improvement Center (CIMMYT) Apdo. Postal 6-641,
06600 Mexico, D.F., Mexico. E-mail: jabfpc@yahoo.com
Mr Marshall Burke, Program on Food Security and the Environment, Stanford University,
Freeman Spogli Institute for International Studies, Encina Hall, 616 Serra St, Stanford,
CA 94305-6055, USA. E-mail: mburke@stanford.edu
Dr Scott Chapman, Commonwealth Scientific and Industrial Research Organization
(CSIRO) Plant Industry, Queensland Bioscience Precinct – St Lucia, 306 Carmody Road,
St Lucia, QLD 4067, Australia. E-mail: scott.chapman@csiro.au
Dr José Crossa, Biometrics and Statistics Unit, Crop Research Informatics Lab, International
Maize and Wheat Improvement Center (CIMMYT) Apdo. Postal 6-641, 06600 Mexico,
D.F., Mexico. E-mail: j.crossa@cgiar.org
Dr Etienne Duveiller, International Maize and Wheat Improvement Center (CIMMYT),
Global Wheat Program, Apdo Postal 6-641, 06600 Mexico, D.F. Mexico. E-mail: e.
duveiller@cgiar.org
Mr Michael Gilbert, Australian Centre for Plant Functional Genomics, University of
Adelaide, Urrbrae, SA 5064, Australia. E-mail: michael.gilbert@acpfg.com.au
Dr Bram Govaerts, International Maize and Wheat Improvement Center (CIMMYT),
Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: b.govaerts@cgiar.org

vii
viii Contributors

Dr Malcolm J. Hawkesford, Centre for Crop Genetic Improvement, Plant Sciences

Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK. E-mail:
malcolm.hawkesford@bbsrc.ac.uk
Dr Dirk Hays, Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen
Blvd., 2474 TAMU, College Station, TX 77843-2474, USA. E-mail: dbhays@neo.tamu.edu
Dr Peter R. Hobbs, Department of Crop and Soil Sciences, 609 Bradfield Hall, Cornell
University, Ithaca NY 14853, USA. E-mail: ph14@cornell.edu
Dr David Hodson, Cereal Rust Monitoring Program, Food and Agriculture Organization of
the United Nations (FAO), Agriculture Plant Production and Protection (AGP) Division,
Viale delle Terme di Caracalla, 00153, Rome, Italy. E-mail: david.hodson@fao.org
Dr Yasukazu Hosen, Japan International Research Center for Agricultural Sciences
(JIRCAS), 1-1 Ohwashi, Tsukuba 305-8686, Japan and International Rice Research
Institute (IRRI), Los Baños, The Philippines. E-mail: y.hosen@cgiar.org
Dr Andy Jarvis, International Centre for Tropical Agriculture (CIAT), Cali, Colombia,
AA6713 and Bioversity International, Regional Office for the Americas, c/o CIAT, Cali,
Colombia, AA6713. E-mail: a.jarvis@cgiar.org
Dr Nobuko Katayanagi, Japan International Research Center for Agricultural Sciences
(JIRCAS), 1-1 Ohwashi, Tsukuba 305-8686, Japan and International Rice Research
Institute (IRRI), Los Baños, The Philippines. E-mail: n.katayanagi@cgiar.org
Professor Peter Langridge, Australian Centre for Plant Functional Genomics, University
of Adelaide, Urrbrae, SA 5064, Australia. E-mail: peter.langridge@acpfg.com.au
Dr Anne Legrève, Université catholique de Louvain, Unité de phytopathologie, Croix du
Sud 2/3, 1348 Louvain-la-Neuve, Belgium. E-mail: anne.legreve@uclouvain.be
Mr Christoph Leibing, International Centre for Tropical Agriculture (CIAT), Cali, Colombia,
AA6713. E-mail: cleibing@gmail.com
Dr David Lobell, Program on Food Security and the Environment, Stanford University,
Energy and Environment Building, 473 Via Ortega, Stanford, CA 94305, USA. E-mail:
dlobell@stanford.edu
Dr Mark Mazzola, United States Department of Agriculture (USDA) Agricultural Research
Service (ARS), Tree Fruit Research Laboratory, 1104 N. Western Avenue, Wenatchee, WA
98801, USA. E-mail: mark.mazzola@ars.usda.gov
Dr Daniel J. Mullan, International Maize and Wheat Improvement Center (CIMMYT),
Apdo. Postal 6-641, 06600 México, D.F., Mexico. E-mail: d.mullan@cgiar.org
Dr Rodomiro Ortiz, International Maize and Wheat Improvement Center (CIMMYT),
Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: r.ortiz@cgiar.org
Dr Ivan Ortiz-Monasterio, International Maize and Wheat Improvement Center
(CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: i.monasterio@cgiar.
org
Professor Martin A.J. Parry, Centre for Crop Genetic Improvement, Plant Sciences
Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK. E-mail:
martin.parry@bbsrc.ac.uk
Dr Thomas Payne, International Maize and Wheat Improvement Center (CIMMYT), Apdo.
Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: t.payne@cgiar.org
Mr Julian Ramirez, International Centre for Tropical Agriculture (CIAT), Cali, Colombia,
AA6713. E-mail: j.r.villegas@cgiar.org
Dr Matthew P. Reynolds, International Maize and Wheat Improvement Center (CIMMYT),
Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico. E-mail: m.reynolds@cgiar.org
Dr Mateo Vargas, Biometrics and Statistics Unit, Crop Research Informatics Lab,
International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641,
06600, Mexico, D.F., Mexico. E-mail: vargas_mateo@hotmail.com
Ir Nele Verhulst, International Maize and Wheat Improvement Center (CIMMYT), Apdo.
Postal 6-641, 06600 Mexico, D.F., Mexico and Katholieke Universiteit Leuven, Department
 Contributors ix

of Earth and Environmental Sciences, Division of Soil and Water Management,

Celestijnenlaan 200 E, 3001 Leuven, Belgium. E-mail: nele.verhulst@gmail.com
Dr Reiner Wassmann, International Rice Research Institute (IRRI), Los Baños, The
Philippines and Research Center Karlsruhe, Institute for Meteorology and Climate
Research (IMK-IFU), Garmisch-Partenkirchen, Germany. E-mail: r.wassmann@cgiar.org
Dr Jeffrey White, United States Department of Agriculture (USDA) Agricultural Research
Service (ARS), ALARC, 21881 N Cardon Lane, Maricopa, AZ 85138, USA. E-mail: jeffrey.
white@ars.usda.gov
Dr Ryan Whitford, Australian Centre for Plant Functional Genomics, University of
Adelaide, Urrbrae, SA 5064, Australia. E-mail: ryan.whitford@acpfg.com.au
 Foreword

This book is very timely. The issues of food security and climate change are both at the top of
the political agenda. The agricultural sector is a significant contributor to greenhouse gas
emissions and changes in climate are projected to affect agricultural productivity and food
security, hence the need to limit greenhouse gases from the agricultural sector, and for the
agricultural sector to adapt to a changing climate.
The last couple of years have been a period of increased food prices, increasing the number
of people going to bed hungry at night to over one billion. The underlying causes of the
increases in food prices are complex and include two factors related to climate change, i.e.
poor harvests due to an increasingly variable climate (e.g. the Australian drought, which
could be linked to human-induced climate change) and the use of food crops for biofuels (e.g.
maize for bioethanol – addressing climate change by replacing fossil fuel energy with bioen-
ergy), as well as increased demand from rapidly growing economies (especially China), higher
energy and fertilizer prices, low food stocks per capita, export restrictions on agricultural
products from a number of significant exporters to protect domestic consumers (e.g.
Argentina, India and Ukraine) and speculation on the commodity futures market. In addi-
tion, many developed country agricultural import tariffs and export subsidies distort global
markets: depressing world prices in some cases, for example via subsidized ‘dumping’ (mak-
ing local production difficult in developing countries); and increasing global prices by inflat-
ing OECD (Organisation for Economic Co-operation and Development) prices.
Some factors impacting food prices are shorter term than others. For example the effects
of adverse weather conditions tend to be relatively short-lived, but recurrent. High prices
stimulate increased production, but rebuilding depleted global stocks to levels that markets
are comfortable with will take years. Longer-term issues include the future cost of energy
and the impact of global warming, which may give rise to more enduring climate change,
more variable weather and more frequent occurrences of extreme weather events leading to
potentially greater agricultural price variability in future. Therefore, a key question is: what
do we need to know and what do we need to do if we are to provide sustainable, nutritious
and affordable food for the world in an environmentally and socially sustainable manner?
This book addresses many of these issues.
The goal of affordable nutritious food for all in an environmentally sustainable manner is
achievable, but it cannot be achieved through current agricultural ‘business as usual’. Instead,
if a large part of the world isn’t to go hungry in the 21st century, we need nothing short of a
new ‘agricultural revolution’, with a more rational use of scarce land and water resources, an

x
 Foreword xi

equitable trade regime, as well as widespread recognition and action on climate change. We
also need to recognize that in this changing world we need new tools, which means increased
investments in agricultural knowledge, science and technology.
It is undeniable that over the past century, agricultural science and new technologies
have boosted production, with enormous gains in yields and reductions in the price of food.
But these benefits have been unevenly distributed; for example, today (i.e. mid-2009) over
one billion people still go to bed undernourished every night, especially in parts of sub-
Saharan Africa and South-east Asia – there have been an additional 100–150 million people
in the last couple of years associated with the increase in food prices and the global economic
downturn. Primarily this is a problem of distribution and local production, but solutions are
going to be increasingly difficult. In coming decades we need to double food availability,
meet food safety standards, enhance rural livelihoods and stimulate economic growth in an
environmentally and socially sustainable manner. All of this at a time when the rate of
increase in productivity per hectare for most cereals is decreasing, when there will be less
labour in many developing countries as a result of HIV/AIDs and other endemic diseases
(e.g. malaria in Africa), when competition from other sectors will make water even more
scarce, when there will be less arable land due to soil degradation and competition from
biofuels, when biodiversity is being lost at the genetic, species and ecosystem level, and
when the climate will be changing, resulting in higher temperatures, changing and more
variable rainfall patterns (more intense rainfall events and less light rainfall events) and
more frequent floods and droughts.
There is no doubt that the Earth’s climate has changed over the past century due to human
activities (use of fossil fuels to produce energy, coupled with unsustainable agricultural and
land-use practices), and future change is inevitable. The magnitude of changes in the Earth’s
climate over the next two to three decades is independent of any post-Kyoto agreement and
is controlled by historic emissions. However, changes in climate beyond the decade of the
2030s are critically dependent upon agreements to reduce global emissions of greenhouse
gases as soon as possible.
This book comprehensively addresses the impact of climate change on crop productivity
and approaches to adapt to both biotic and abiotic stresses, as well as approaches to reduce
greenhouse gases. Crop productivity will not only be affected by changes in climatically
related abiotic stresses (i.e. increasing temperatures, decreasing water availability, increas-
ing salinity and inundation) and biotic stresses (such as increases in pests and diseases), but
also changes in the atmospheric concentration of carbon dioxide, acid deposition and ground
level ozone. Hence, a key challenge is to assess how crops will respond to simultaneous
changes to the full range of biotic and abiotic stresses. Responding to these challenges will
require advances in crop research and the adoption of appropriate technologies.
The new agricultural revolution needed to meet this challenge will require a fundamental
rethink of the role of agricultural knowledge, science and technology. Agriculture can no
longer be thought of as production alone, but the inescapable interconnectedness of agricul-
ture’s different economic, social and environmental roles and functions must also be expli­
citly recognized.
Thankfully, many of the technologies and practices we need to meet the challenge of sus-
tainable agriculture already exist. For instance, we know how to manage soil and water more
effectively to increase water retention and decrease erosion; we already have access to micro-
biological techniques to suppress diseases in soils; and conventional biotechnology (plant
breeding) can help us produce improved crop varieties. But climate change and new and
emerging animal diseases are throwing up problems that we have not considered before and
which will need advances in agricultural knowledge, science and technology to address. In
addition, we need to use technologies that already exist to reduce postharvest loss and
improve food safety. We need to integrate, as appropriate, local and traditional knowledge
with formal knowledge, ensuring that the needs of the small-scale farmer are addressed.
xii Foreword

Climate change has the potential to irreversibly damage the natural resource base on
which agriculture depends, and in general adversely affects agricultural productivity. While
moderate increases in temperature can have small beneficial effects on crop yields in mid- to
high latitudes, in low latitudes even moderate temperature increases are likely to have nega-
tive effects on yields. Water scarcity and the timing of availability will increasingly constrain
production, and it will be critical to take a new look at water storage to cope with more
extreme precipitation events, higher intra- and inter-seasonal variations (floods and
droughts) and increased evapotranspiration. Climate change is already affecting, and is
likely to increase, invasive species, pests and disease vectors, all adversely affecting agricul-
tural productivity. Advances in agricultural knowledge, science and technology will be
required to develop improved crop traits, for example temperature, drought, pest and salt
tolerance. In addition, it will be critical to reduce greenhouse gas emissions from the agricul-
tural sector – methane from livestock and rice and nitrous oxide from the use of fertilizers.
And while biofuels can offer potential benefits (i.e. energy security, reducing greenhouse
gas emissions and improving rural economies) the production of first generation biofuels,
which are predominantly produced from agricultural crops (e.g. bioethanol from maize, and
biodiesel from palm oil and soya), can raise food prices and reduce our ability to alleviate
hunger. There is also considerable debate over the environmental impact of biofuels, includ-
ing the degree to which greenhouse gas emissions are reduced, and their impact on biodiver-
sity, soils and water. Increased public and private investments are needed to develop future
generation biofuels, such as cellulosic ethanol and biomass-to-liquids technologies, so that
cheaper and more abundant feedstocks can be converted into biofuels, potentially reducing
the demands for agricultural land.
Currently the most contentious issue in agricultural science is the use of recombinant
DNA techniques to produce transgenic products because there is not widespread agreement
on the environmental, human health and economic risks and benefits of such products.
Many believe that less technology and intervention is the answer. But against a backdrop of
a changing climate and the threat of even larger parts of the world going hungry, it is clear
that integrated advances in biotechnology, nanotechnology, remote-sensing and communi-
cation technologies for instance, in combination with agroecological practices, will be impor-
tant in providing opportunities for more resource-efficient and site-specific agriculture.
Advances in genomics will play a critical role in traditional plant breeding as well as in pos-
sible options for genetically modified (GM) crops. No technology should be ruled out; how-
ever, it will be critical to assess the risks and benefits of any technology on a case-by-case
basis. This book explores the full range of techniques that can be used to develop the crop
traits needed to adapt to a changing climate.
Today’s hunger problems can be addressed with appropriate use of current technologies,
emphasizing agroecological practices (e.g. no/low till, integrated pest management (IPM)
and integrated natural resource management (INRM)), combined with decreased posthar-
vest losses, and trade reform and rural development more broadly. Small-scale farmers need
access to the best seeds, financing and access to markets, and we need to create opportuni-
ties for innovation and entrepreneurship and invest in science and technology and exten-
sion services to meet their needs. We also need to provide payments to the farmer for
maintaining and enhancing ecosystem services, and to recognize the important role of
women and empower them through education, access to financing and property rights. But
doubling food availability over the coming decades in the context of climate change and
other stresses will require advances in crop research and improved agricultural practices,
with emphasis on the sustainable management of water and soils.
Meeting the goal of affordable nutritious food for all in an environmentally sustainable
manner is achievable, but we will need to decrease the vulnerability of agricultural productiv-
ity to projected changes in climate, develop the next generation of biofuels and transform the
trade system to benefit the small-scale farmer. The future is not preordained, but is in our

xii
 Foreword xiii

collective hands. While we can build upon our successes, we must also recognize that an
extrapolation of business-as-usual will not suffice. Instead, we need to be bold enough to
rethink agriculture. Most importantly, if we are to help today’s and tomorrow’s poor and
disadvantaged, we need to acknowledge that the time to act is now.

Robert T. Watson
Chief Scientific Advisor
UK Department of Environment, Food and
Rural Affairs
and Strategic Director
Tyndall Centre at the University of
East Anglia
 Preface

In light of population growth and climate change, investment in agriculture is the only way
to avert wide-scale food shortages or, in the worst-case scenario, catastrophic human suffer-
ing. Assuming investment is forthcoming, maintaining food security will require crop scien-
tists to integrate and apply a broad range of strategies. These include tried and tested
technologies such as conventional breeding and agronomy as well as new approaches such as
molecular genetics and conservation agriculture. Each topic in this book has been selected
for its potential contribution to maintain and increase crop productivity in unpredictable
environments, providing readers with an overview of the state of the art in respective fields.
Examples of successful applications as well as future prospects of how each discipline can be
expected to evolve over the next 30 years are presented. The objectives of the book are two-
fold: (i) to lay out some basic concepts for crop scientists who, given changes in crop environ-
ments, may find it necessary to explore new disciplines in which they lack practical experience;
and (ii) to provide an overview of the essential disciplines required for sustainable crop pro-
duction for policy makers, academics and students of agriculture.

xiv
 Dedication

This book is dedicated to Norman E. Borlaug, father of the Green Revolution, for a life dedi-
cated to improving food security for resource-poor people worldwide.

xv
 Acknowledgement

The editor and authors are indebted to Debra Eaton for careful proofreading of chapters and
providing technical editing advice.

xvi
 1
Adapting Crops to Climate
Change: a Summary
Matthew P. Reynolds and Rodomiro Ortiz
The Intergovermental Panel on Climate
Change (IPCC, 2009) indicates that rising
temperatures, drought, floods, desertifica-
tion and weather extremes will severely
affect agriculture, especially in the develop-
ing world. While the convergence of popula-
tion growth and climate change threatens
food security on a worldwide scale, the
opportunity also exists to address the perni-
cious threat of famine. Indeed the prerequi-
sites to develop a globally coordinated effort
to ensure long-term food security are avail-
able for the first time in human history.
Namely: (i) the realization that agricultural
problems worldwide have a common scien-
tific basis; (ii) a vast and expanding database
encompassing all disciplines that impinge
on agricultural productivity; (iii) a de facto
network of agricultural scientists working in
almost every country in the world; and (iv)
unprecedented opportunities for communi-
cation, data analysis and investment. These
elements, the indisputable fruits of an
industrialized global economy, were not
available to our predecessors, which is prob-
ably why climate change in history spelt
death. For example, analysis of high-resolu-
tion palaeoclimatic data – ad 1400–1900 –
showed that in both Europe and China,
long-term weather patterns were strongly
linked to the frequency of wars (Zhang et al.,
2007), while recent analysis in Africa indi-
cates that global warming increases risk of
civil war (Burke et al., 2009).
Agricultural researchers worldwide are,
therefore, working to mitigate these and
other effects of climate change to increase
productivity within a finite natural resource
basis. Assuming investment is forthcoming,
maintaining food security in the face of
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 1
population growth and climate change will
require a holistic approach that includes
stress-tolerant germplasm, coupled with
sustainable crop and natural resource
management as well as sound policy inter-
ventions. There will be duplication of effort
as regions struggle with parallel challenges;
however, judicious public investment can
reduce redundancy of effort permitting local
organizations to focus on adaptive research.
The Green Revolution was precipitated by a
sense of urgency about famine in South Asia,
yet has benefited millions of farmers world-
wide, especially in resource-constrained
countries (Lipton and Longhurst, 1989;
Evenson and Gollin, 2003). Although these
impacts were achieved with modest invest-
ment, the more universal problem of climate
change will require backstopping from a
larger segment of the scientific and develop-
ment assistance communities if predicted
levels of demand for staple foods are to be
met under progressively less favourable
conditions (Federoff et al., 2010). The topics
in this book have been selected to cover the
broad range of disciplines that will need to
be implemented as part of a consolidated
research effort to maintain and increase crop
productivity in unpredictable environ-
ments.
Predictions of Climate Change and its
Impact on Crop Productivity
In the first section of the book, chapters by
Lobell and Burke (Chapter 3) and Jarvis et
al. (Chapter 2) address predictions of climate
change over the next 30+ years and their
likely biological and economic consequences
2 M.P. Reynolds and R. Ortiz

in the context of crop productivity. Their • While projections for a few countries
main points are summarized as follows. with northerly latitudes indicate net
Developing countries will be affected positive impacts of climate change,
most for three reasons: (i) climate change pro­jections for most developing coun-
will have its most negative effects in tropical tries are negative.
and subtropical regions; (ii) most of the • Only ‘best-case’ scenarios predict no net
predicted population growth to 2030 will effect of climate change on global cereal
occur in the developing world (United yields by 2030 but predictions beyond
Nations Population Division DoEaSA, 2009); that time frame are much more pessimis-
and (iii) more than half of the overall work tic.
force in the developing world is involved in
On a more positive note, Lobell and Burke
agriculture (FAO, 2005).
(Chapter 3) also state that an important
While anthropogenic effects on climate
factor in terms of maintaining productivity
have been apparent for several decades,
in the face of climate change will be the way
modelling future climate change is not an
farmers adapt their cropping systems: for
exact science due to the complexity and
example by diversifying when faced by
incomplete understanding of atmospheric
increased risk, or by adopting new technolo-
processes. None the less, there is broad
gies derived from centrally planned efforts,
agreement that, in addition to increased
such as cultivars bred to resist biotic and
temperatures (see Plate 1), climate change
abiotic stresses as well as improved and more
will bring about regionally dependent
sustainable cropping practices that permit
increases or decreases in rainfall (see Plate
the genetic potential of new cultivars to be
2), an increase in cloud cover and increases
realized. These issues are addressed in subse-
in sea level. Extreme climate events will also
quent chapters.
increase in intensity or frequency, such as
higher maximum temperatures, more
intense precipitation events, increased risk Adapting to Biotic and Abiotic
and duration of drought, and increased peak
Stresses Through Crop Breeding
wind intensities of cyclones. Predictions in
sea level rise indicate that this will continue
One of the most challenging aspects of
for centuries after temperatures stabilize,
adapting crops to climate change will be to
causing flooding of coastal lands and salini-
maintain their genetic resistance to pests
zation of soils and subsurface water in
and diseases, including weeds, herbivorous
coastal regions.
insects, arthropods, nematodes, fungi,
Models of crop response to climate change
bacteria and viruses. Rising temperatures
mainly consider temperature, soil moisture
and variations in humidity affect the diver-
and increased carbon dioxide. However,
sity and responsiveness of agricultural pests
many other processes not easily incorp­
and diseases and are likely to lead to new
orated into models could potentially have
and perhaps unpredictable epidemiologies
significant effects including: pests and
(Gregory et al., 2009). Legrève and Duveiller
diseases, brief exposures of crops to very
in Chapter 4 explain that, for a disease to
high temperatures, elevated ozone, loss of
occur, three essential components are
irrigation water, and increase in inter-annual
required simultaneously: a virulent patho-
climate variability associated with monsoons
gen, a susceptible host and a favourable
and phenomena like El Niño. The model
environment – often referred to as the
outputs, while encompassing a wide range of
‘disease triangle’. Climate change, as well as
potential outcomes, tend to have the follow-
sometimes fulfilling the last link of that
ing in common:
triangle, can also drive evolutionary change
• The yield potential of staple foods will in pathogen populations by forcing changes
decline in most production environments in reproductive behaviour. Changes in crop-
and commodity prices will rise. ping systems can lead to the development of
 Adapting Crops to Climate Change 3
new pathogens, for example through inter-
specific hybridization between introduced
and endemic pathogens, and history has
shown how devastating such events can be
to food security. Legrève and Duveiller point
out that strategies to limit the effect of
climate change on pests and diseases do not
fundamentally differ from existing inte-
grated pest management practices, although
there will need to be a much greater empha-
sis on modelling and forecasting systems,
while breeding for host resistance will
continue to have a pivotal role. They cite the
rapid response of the scientific community
to the dispersal of the Ug99 wheat stem rust
race as an example of how internationally
coordinated monitoring and breeding efforts
can mitigate the threat of potential epidem-
ics (Singh et al., 2008).
The major abiotic stresses that are
expected to increase in response to climate
change are heat, drought, salinity, waterlog-
ging and inundation. The former are
addressed by Reynolds et al. in Chapter 5.
The responses of crops to these two abiotic
stresses have a number of similarities,
although the genetic basis is not necessarily
the same. Growth rate is accelerated due to
increased plant temperature, which reduces
the window of opportunity for photosynthe-
sis since the life cycle is truncated, while
both heat and drought stress may also
inhibit growth directly at the metabolic
level. Furthermore, harvest index may be
reduced if reproductive processes are
impaired by stress that occurs at critical
developmental stages. Genetic improvement
under these environments has been achieved
by incorporating stress-adaptive traits into
good agronomic backgrounds (Richards,
2006). As understanding of the physiologi-
cal and genetic basis of adaptation is
improved, this approach can be expanded in
conjunction with molecular approaches to
tackle even some of the most challenging
aspects of climate change, such as adapta-
tion to higher temperatures without loss of
water-use efficiency, and tolerance to sudden
extreme climatic events or combinations of
stress factors. Given the complexity of the
target environments themselves, as well as
the constant fluxes in weather and other
factors such as biotic stresses, plant selec-
tion will for the foreseeable future require
empirical approaches such as multi-location
testing. A number of crop-specific examples
of successful breeding approaches are
discussed as well as the potential of biotech-
nology to improve the efficiency of breeding
through marker assisted selection (MAS),
and the use of genetic resources to broaden
the genetic base of crop species.
In Chapter 6, Mullan and Barrett-Lennard
explain that climate change is expected to
reduce water availability in general making
the use of low-quality water resources more
common. Water-stressed hydrological basins
already affect approximately 1.5–2.0 billion
people (Bates et al., 2008), a figure expected
to increase substantially leading to problems
of soil salinity and sodicity. Climate change
will also bring inundation in low-lying land-
scapes associated with increased runoff from
tropical storms while sea level rise will
increase levels of salinity, waterlogging and
inundation in coastal regions. The authors
go on to explain that soil salinity affects
plant growth and survival because ions
(mainly Na+ and Cl–) increase in the soil
solution, causing osmotic stress, while their
accumulation in plant tissue impairs metab-
olism. Waterlogging leads to the displace-
ment of air from the soil pores, leading to
hypoxia (O2 deficiency, which is especially
detrimental to root growth and eventually
impairs all aspects of plant growth). A range
of adaptive traits is discussed; however, large
areas of land subject to salinity and water-
logging are still to benefit from plant breed-
ing. Climate change is likely to increase these
areas, making it imperative to address the
genetic challenges of productivity in such
environments.
It is important to remember that water-
logging and salinity, which already constrain
productivity on hundreds of millions of
hectares worldwide, also have potential
engineering solutions (Bhutta and Smedema,
2007). Although beyond the scope of this
book, given the scale of the problem and the
challenges ahead associated with population
growth and climate change, engineering
interventions will require major investment;
failure to do so will lead to desertification
4 M.P. Reynolds and R. Ortiz
and an overall net reduction in potential
global productivity.
Development and dissemination of new
germplasm can be a slow process without
public sector investment that provides new
genotypes to seed companies. The most
comprehensive germplasm development
and deployment exercise ever undertaken
was that associated with the Green
Revolution rice and wheat cultivars, and its
legacy includes some of the largest and most
effective breeding programmes in the world
for the major cereal crops. Chapter 7 by
Braun et al. describes how these global
breeding programmes function – using
examples drawn from maize, rice and wheat
– and their unique remit to provide useful
new cultivars for a range of environments
that already encompasses many of the stress
factors that climate change will make more
widespread in years to come. The authors
explain the benefit of genetic resources as a
global public good, implemented through an
extensive system of international nursery
trials with a breeding hub, free sharing of
germplasm, collaboration in information
collection, the development of human
resources, and an international collaborative
network. Broad-based, widely adapted,
stress-tolerant cultivars, coupled with
sustainable crop and natural resource
management, will provide means for farm-
ers to cope with climate change and benefit
consumers worldwide. Chapter 7 also
provides an overview on climate change
impacts on the three main cereals that feed
the world as well as ongoing breeding
research to adapt the crop to the expected
warm and drought-prone environments
where they will grow. The authors end their
chapter by discussing the future of crop
mega-environments (MEs) as a breeder’s
tool. MEs are broad, often non-contiguous
or transcontinental areas with similar biotic
or abiotic stresses, cropping systems,
consumer preferences and volumes of
production. Braun et al. conclude that under
new climate change scenarios the ME can be
refined geographically to address evolving
needs of various production systems.
Because agriculture is a potential contrib-
utor to climate change, it is pertinent to
consider mitigation strategies as well as
those of adaptation. This is addressed in the
context of crop management in the next
section of the book, while Parry and
Hawkesford discuss breeding strategies in
Chapter 8. Genetic manipulation to enhance
the specificity of Rubisco for CO2 relative to
O2 and to increase the catalytic rate of
Rubisco in crop plants would increase yield
potential, thereby increasing input-use effi-
ciency of cropping systems as a whole,
because efficiencies of scale can be expected
in terms of use of nitrogen, diesel fuel, etc.
Similarly, introducing C4 photosynthesis
into C3 crops can be expected to increase
yield potential at warmer temperatures and
moderate levels of water deficit, though this
is recognized to be a long-term research
undertaking due to the need for introducing
multiple structural and metabolic traits into
C3 plants. Selecting for genetic mechanisms
that improve N-use efficiency can also miti-
gate climate change by reducing greenhouse
gas (GHG) emissions. Transgenic approaches
that allow plant roots to release inhibitory
compounds to suppress nitrification in the
rhizosphere could substantially decrease the
emission of nitrous oxide (N2O), one of the
most potent GHGs.
Sustainable and Resource-
conserving Technologies for
Adaptation to and Mitigation of
Climate Change
Sustainable and resource-conserving crop
management technologies offer several
major benefits under climate change. These
include:
1.  Practices such as reduced tillage in
combination with crop residue retention can
buffer crops against severe climatic events,
for example, by increasing water harvest and
thereby offsetting water shortages that will
intensify as global temperatures rise.
2.  In addition, by improving the overall
environment for root growth, such practices
permit the genetic potential of improved
cultivars to be more optimally expressed
 Adapting Crops to Climate Change 5
helping to close yield gaps that may already
exist.
3. Diversification of cropping systems helps
to control soilborne diseases.
Longer-term benefits include:
4.  Reduced emission of GHGs through
greater precision in the application of N and
water as well as reduced use of diesel fuel.
5.  More robust soils, which are less prone
to becoming degraded even as climate
change increases the need for more inten-
sive cultivation in still productive regions.
Ortiz-Monasterio et al. focus Chapter 9
on the management options that could miti-
gate methane (CH4) or N2O emissions from
the intensive cropping systems where they
are grown. The chapter describes the main
elements of each of the cropping systems that
affect the environment and what alternatives
are available for reducing their impact on
climate change, for example mid-season
drainage in rice paddy fields, or best practices
to manage N use in maize and wheat fields.
The authors also explain how conservation
agriculture (CA) and other sustainable farm-
ing practices can reduce GHG emissions and
their potential for sequestering C. For exam-
ple, one of the best options for mitigating
GHG emissions from rice fields includes
management that leads to greater oxidative
soils, allows organic decomposition under
more aerobic conditions, and uses zero till-
age, which seems to be very practical due to
cost and labour savings. N rates, timing,
source and placement in maize and wheat
cropping systems could also assist in mitigat-
ing N2O emissions. In this regard, spectral
sensor-based N management can be used to
establish the optimum N fertilization rates,
thereby minimizing the risk of over fertiliz-
ing.
Hobbs and Govaerts in Chapter 10 point
out that while resource conserving technolo-
gies help mitigate climate change by reduc-
ing GHG emissions, agronomic practices
must also protect against extreme weather
events such as drought, flooding, etc., and
prevent further soil degradation. They
provide evidence that adoption of practices
such as CA can achieve both objectives
through reducing the surface tillage to a
minimum while introducing residue reten-
tion and crop rotations into the system.
Their combined effect is to protect the soil
from water and wind erosion, reduce water
runoff and evaporation, increase infiltration
of water thereby reducing inundation and
salinity build up, and, in combination with
appropriate crop rotation, enhance the
physical, chemical and biological properties
of the soil (Hobbs et al., 2008). Additional
benefits include increased N-use efficiency
and less use of fossil fuel – associated with
tillage operations – and therefore reduced
GHG emissions. Under CA, species diversity
in the soil is increased creating more possi-
bilities for integrated pest control. The pres-
ence of increased biological activity also
improves nutrient cycling, water infiltration
and soil physical properties (Verhulst et al.,
2010).
As already mentioned, climate change will
influence the spectrum of diseases that
normally affect a crop species while increas-
ing selection pressure on pre-existing threats.
In Chapter 11, Mark Mazzola points out that,
compared with diseases affecting aerial plant
parts, soilborne diseases are more difficult to
detect and to control. That given, it is
extremely challenging to select for genetic
resistance, making crop management strat-
egies an essential component of the control
of soilborne diseases. The most effective
control method has been soil fumigation
(mostly with methyl bromide), which has
highly detrimental environmental conse-
quences. Alternatives such as host resistance
or application of microbiological control
agents are generally effective towards a more
limited and targeted pathogen population
but operate on sound ecological principals
(Weller et al., 2002). Naturally disease-
suppressive soils also exist associated with
the presence of resident microorganisms
(Cook and Baker, 1983), and such soils can
even be used to ‘seed’ other soils to increase
their capacity for suppression. In addition,
approaches such as introducing organic resi-
dues including green manures, as well as
growing alternate crops in rotations can
increase a soil’s ability to suppress pathogens.
In this context, practices associated with CA,
6 M.P. Reynolds and R. Ortiz
including crop rotation and residue retention,
offer some strategies that can positively influ-
ence disease-suppressive soil characteristics.
Likely pressures on disease evolution associ-
ated with climate change as well as intensifi-
cation of cropping systems, in conjunction
with restrictions on the use of chemical
control methods, make it opportune to
further develop this field as a viable strategy
to control soilborne diseases that are likely to
escalate as agricultural systems are intensi-
fied to match growing demand.
New Tools for Enhancing Crop
Adaptation to Climate Change
The final section of the book presents tools at
the ‘cutting edge’ of agricultural technology.
Increased integration of these approaches
into breeding programmes is inevitable, at
least for those providing unequivocal bene-
fits. Recent advances in genomics research
address the multigenic nature of plant abiotic
stress adaptation, including the potential of
genetic engineering of new traits which are
not amenable to conventional breeding
(Ortiz, 2008; Federoff et al., 2010). The
marriage of geographic information systems
(GIS) with sophisticated statistical and
modelling tools is also addressed as a means
to better target breeding efforts through
enhanced understanding of the interaction of
complex and changing environments with
genes and genomes.
As pointed out by Whitford et al. in
Chapter 12, important new tools are becom-
ing available to assist with breeding for
climate change. Chapter 12 is also helpful in
introducing some of the basic concepts of
biotechnology. The authors provide details
of induced genetic variation in crops, such as
introgression through backcrossing, amphi­
diploidy, mutagenesis, in vitro culture and
transgenics. Recent advances in genomics
are highlighted as tools to dissect stress
adaptive mechanisms both metabolically
and genetically. The authors also indicate the
use of model plant systems and their ability
for predicting, through modelling, traits in
other crops. Molecular breeding tools such
as marker-aided backcrossing (MABC) or
MAS are presented as the promising new
additions to the breeder toolkit. Other
methods such as early generation MAS, in
silico breeding and metabolite-assisted
breeding are also described. The analysis of
diversity and population dynamics are other
important uses of DNA markers for design-
ing knowledge-led plant breeding approaches
and managing genebank collections for
further use in crop improvement. High-
throughput genotyping and phenotyping
are also important tools for accelerating
both population improvement and cultivar
development. The authors explain in detail
the steps of transgenic approaches as well as
the advances in gene discovery technology
that can assist plant-breeding endeavours to
address climate change. The chapter ends by
discussing investments on capacity building
by both private and public sectors, and access
to technology, whose deployment may be
affected by intellectual property issues and
regulatory systems.
While GIS and crop modelling are essen-
tial tools in predicting climate change, the
same tools have a variety of other applica-
tions that can assist with many of the
research areas discussed in previous chap-
ters. Chapter 13 by Hodson and White
demonstrates a central role for these tech-
nologies, including: (i) interpolating meteor-
ological data to define climatic zones; (ii)
estimating spatial variation in soils to infer
agronomic potential; (iii) defining climatic
suitability zones of pests and diseases to
predict the likelihood of their incidence; and
(iv) identification of potential collection sites
of crop wild relatives in terms of likely genetic
potential based on environmental selection
pressures. One of the major benefits of
improved characterization of target environ-
ments is that resources for crop improve-
ment can be deployed more effectively. Crop
simulation models simulate the key physio-
logical processes believed to determine crop
performance so as to predict crop develop-
ment, adaptation and performance.
Therefore, in combination with GIS data-
bases, which capture the heterogeneity of
environments in both space and time, crop
modelling permits a more systematic
approach to understanding how genotypes
 Adapting Crops to Climate Change 7
interact with environmental factors and are
likely to perform in response to climatic as
well as other environmental variables. Given
the considerable challenges facing crop scien-
tists to maintain food security, it can be
expected that application of these tools will
soon become routine in crop research. A
recent application has been to monitor shift-
ing abiotic and biotic stress distributions for
major cereal crops, indicating likely changes
in the size and distribution of target environ-
ments in the near future; this has important
implications for how breeding resources
must be redeployed to meet demands 10–20
years from now as outlined by Braun et al.
(Chapter 7).
As climate changes and becomes less
predictable, the use of statistical tools to
achieve a better understanding of how culti-
vars interact with environment will become
invaluable both in deploying genes and germ-
plasm and in defining ‘weak links’ as targets
for research investment. Chapter 14 by
Crossa et al. provides an overview of several
statistical models and their application for
explaining the climatic and genetic causes of
genotype × environment (GE) interaction.
Their advantages and shortcomings are also
highlighted by the authors, who claim that
multi-environment trials are very important
for breeding cultivars with general or specific
adaptation and yield stability, studying GE
interactions, and predicting the performance
of new cultivars in future years and new loca-
tions. They indicate that data ensuing from
such trials should include not only pheno-
typic measurements of cultivars across envi-
ronments but also climatic and soil data as
well as molecular markers representing
genetic data. Some examples are given to
illustrate the use of appropriate statistical
models for gaining better insights about the
GE interaction in multi-environment trials.
Conclusions
Current trends in population growth suggest
that global food production is unlikely to
satisfy future demand under predicted
climate change scenarios unless rates of crop
improvement are accelerated (or radical
changes occur in patterns of human food
consumption). The situation is generally
more serious in less developed countries
where agroecosystems are already fragile,
investment in agriculture is limited, and
climate change is predicted to have its most
devastating effects. The following crop-
oriented technical solutions can be imple-
mented to increase food security:
• application of crop and land management
practices that maximize sustainable
productivity from a given natural resource
and permit the full genetic potential of
cultivars to be realized;
• implementation of both management and
breeding strategies to reduce GHG emis-
sions from cropping systems – thereby
mitigating negative impacts of agriculture
on climate change – such as precision
application of inputs and genetic enhance-
ment of input-use efficiency;
• crop breeding with emphasis on rapid
deployment of lines adapted to the
harsher environments anticipated from
climate change models, while improving
genetic yield thresholds in general;
• systematic evaluation of genetic resources
to better target their use in cultivar
improve­ment;
• investment in characterizing target agro­
ecosystems (taking into account cultiva-
tion, climatic, biotic and edaphic factors)
to permit different models of genetic
adaptation to be systematically evaluated;
• integrated use of research techniques
(e.g. remote sensing for precision pheno-
typing, networks of field operations,
state-of-the-art molecular techniques,
etc.) that will permit genome analysis to
be more precisely linked to the adaptive
responses of crops;
• determination of the theoretical limits to
resource-use efficiency of cropping
systems (including nutrients, water and
light) to help establish realistic research
goals when estimating potential produc-
tivity in future climate scenarios; this
should take into account crop response
and potential adaptation to extreme
climatic events;
• monitoring and modelling the spread of
diseases and pests in response to climatic
8 M.P. Reynolds and R. Ortiz
factors to reduce crop losses and reduce
the risk of epidemics; and
• establishment of research consortia
whereby interest in solving a common
problem brings together complementary
skills and research platforms.
In summary, the gap between current and
achievable yields must be closed through
breeding and natural resource management
to reduce the risk of catastrophic food
shortages­.
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 2
Scenarios of Climate Change
Within the Context of Agriculture

Andy Jarvis, Julian Ramirez, Ben Anderson,

Christoph Leibing and Pramod Aggarwal

Abstract
This chapter provides an overview of global climate models and their predictions for climate through
the 21st century. The review examines the scientific basis of global climate modelling, including the
bases for uncertainty in future climate projections. A summary of the Special Report Emissions
Scenarios (SRES) is also provided. The current scientific knowledge on climate change points to
increases in temperature of 1–3°C to 2050 combined with some complex spatially explicit changes in
rainfall. There remains high uncertainty in predictions of extreme events, especially hurricanes. The
chapter then looks at the likely impacts of climate change on agricultural productivity, pest and disease
prevalence, and CO2-based fertilization. The impacts on crop productivity are likely to be negative.
While moderate increases in temperature may bring about moderate increases in productivity, beyond
1°C of warming the literature tends to agree that impacts will be negative. However, possible
CO2-fertilization effects may cancel out these losses, although significant debate exists as to the extent
of CO2 fertilization to expect. While most literature predicts increases in the prevalence of agricultural
pests and diseases, only a handful of studies have quantified possible impacts and further research is
needed in this area.

Introduction providing greater certainty in predictions of

Agriculture depends on a favourable climate,
hence is among the sectors of the global
economy­ where most concern currently lies
in the context of climate change in order to
maintain global food security, and avoid
large-scale human suffering in developing
countries where significant portions of gross
domestic product (GDP) are dedicated to
agricultural production and where rural popu-
lations are most vulnerable (Mertz et al.,
2009). The Intergovernmental Panel on
Climate Change (IPCC) Fourth Assessment
Report (FAR) (IPCC, 2007) stated that there is
now little doubt that human-induced climate
change is a reality, and identified agriculture
as a critical sector. Unfortunately, in the Third
Assessment Report (TAR) (IPCC, 2001) there
was considerable uncertainty as to the likely
impacts of climate change on agriculture.
Considerably more literature contributed to
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 9
climate change impacts in agriculture for the
FAR, yet the certainty levels were still only
classified at the ‘moderate’ level in IPCC
speak. Since the FAR in 2007, the volume of
literature on the likely impacts of climate
change has increased considerably, hence this
chapter summarizes IPCC findings and
provides an update on the state of knowledge
of expected changes in climate and the result-
ant impacts on agriculture.
This chapter is divided into two main
sections: scenarios of climate change; and the
expected impacts on agricultural production.
We start by providing a brief explanation of
the available methods for developing climate
change scenarios, summarizing the current
state of play and likely future developments.
The chapter then provides a summary of what
the models say about the future climate. Both
global and regional perspectives are taken,
with summary tables describing the likely
10 A. Jarvis et al.
impacts in the two windows of study. We
make special effort to interpret the latest
results from both global climate models
(GCMs) and regional climate models (RCMs),
taking an agricultural perspective. We do this
by looking at variables relevant to agricultural
production potential, agronomic manage-
ment and pest/disease presence and preva-
lence, and we also look at some specific
extreme events for which agriculture is espe-
cially exposed. The second section of the
chapter examines the impacts that the
expected changes in climate will have on crop
production, addressing three specific issues.
First, a summary of the state of knowledge on
the direct impacts on crop yields, taking
advantage of recent studies which have broad-
ened our knowledge base on the subject. We
then look at the impacts on agricultural pests
and diseases, and finish by examining the
likely positive impacts of CO2 fertilization on
productivity. The chapter concludes with a
synthesis of findings, and identifies some key
areas for future research to fill the knowledge
gaps that still exist.
Climate Change Predictions
The IPCC TAR (2001) provided a baseline for
the prediction of climatic changes at broad
scales by using historical measurements and
future predictions made by several global
circulation models or GCMs in addition to
what the first and second assessment reports
had previously outlined (IPCC, 1990, 1995),
but included the definitions of more polit-
ically oriented scenarios (i.e. the Special
Report on Emissions Scenarios (SRES)
scenarios; IPCC, 2000) rather than the IS92
emission scenarios described in the first and
second assessment reports. Working group I
(WGI) reported:
• average diurnal temperature had increased
by 0.6°C in the 20th century, with a signif-
icant increase from 1910 to 1945, followed
by a slight decrease during the period
1945–1965, and a severe increase from
1976 to 2000;
• increases in sea level between 0.1 and
0.2 m;
• geographically differentiated increases
and decreases in precipitation of at least
1% per decade;
• increases in frequency and intensity of
heavy rainfall events, increase in cloud
cover; and
• reductions in low temperature extreme
events and increases in high temperature
extreme events such as El Niño-Southern
Oscillation (ENSO).
WGI also pointed out that modelling of
climatic changes may involve uncertainties
mainly because the parameterization of
GCMs is still not perfect and because Earth
processes still cannot be perfectly simulated
(especially in regard to the interaction
between clouds, radiation and aerosols).
Nevertheless, the report did mention a
significant improvement on the accuracy of
past prediction of climate based on Earth
processes modelled by the different GCMs.
WGI, in reference to the TAR, concluded by
stating that results of the models suggest
that average surface temperature is likely to
increase by between 1.4 and 5.8°C over the
period 1990–2100, with general accordance
between the different models for each single
emission scenario. Northern high altitudes
are presenting the highest warming rates
during winter periods; precipitation will
probably increase as a global average, but
with significant regional differentiation (i.e.
northern mid- to high latitudes presenting
increases, and low latitudes presenting
significantly different spatial patterns).
Particular attention is paid to likely
changes on extreme events and sea level
alterations. It is reported with high to very
high confidence that in the 1990–2100
period most extreme events will increase in
intensity or frequency, or both. The report
predicts higher maximum temperatures and
a greater number of hot days, higher mini-
mum temperatures and fewer cold days,
reduced diurnal temperature ranges, more
intense precipitation events, increased risk
of drought in summer periods, increases in
peak wind intensities of cyclones, and
increases in mean and peak precipitation
intensities of tropical cyclones. On top of
that, sea level is predicted to increase by
 Scenarios of Climate Change Within Agriculture 11
0.09–0.88 m for the full range of SRES
scenarios (IPCC, 2001).
This section provides a brief summary of
the far more complete analysis of expected
changes in climates contained in the IPCC
FAR (2007). In mid- to high-latitude regions,
models predict moderate to medium local
increases in temperature (1–3°C) along with
associated CO2 increase and rainfall changes
to 2050, while in low-latitude regions, simi-
lar temperature changes (1–2°C) but far
more complex spatial changes in rainfall are
expected. Projected changes in the frequency
and severity of extreme climate events have
important consequences for food and
forestry production and food insecurity in
addition to impacts of projected mean
climate (high confidence).
Global circulation models, SRES
emissions scenarios and uncertainty
Global circulation models (GCMs)
Global circulation models, also often referred
as ‘global climate models’, ‘general circula-
tion models’ or simply GCMs, are based on
well-established physical principles and have
been demonstrated to reproduce observed
features of recent (IPCC, 2001, 2007) and
past climatic changes accurately as evalu-
ation methods have become available (IPCC,
2007; Pierce et al., 2009). Currently, more
than a dozen centres around the world
develop climate models to enhance our
understanding of climate and climate change
and to support the IPCC activities (IPCC,
2001, 2007; Reichler and Kim, 2008). Several
GCMs have now been evaluated by several
authors (Lin et al., 2006; Neelin et al., 2006;
Chou et al., 2008; Cayan et al., 2009; Xavier
et al., 2009) and there is now considerable
confidence that atmosphere–ocean general
circulation models (AOGCMs) provide cred-
ible quantitative estimates of future climate
change, particularly at continental and larger
scales. Confidence in these estimates is
higher for some climate variables (e.g.
temperature) than for others (e.g. precipi-
tation) (IPCC, 2007; Chou et al., 2008). The
main improvements recently include:
• Incorporation of more complex climate
processes, including water vapour, sea–ice
dynamics and ocean heat transport.
• More satisfactory simulations of current
climate.
• Simulations that include effects of natural
and anthropogenic forcing.
• Model simulations of ENSO and other
extreme events have been substantially
improved.
• Enhanced scrutiny of models due to more
global access to them, producing a diver-
sity of evaluation perspectives and more
detailed approaches, ranging from yearly
to daily evaluations of forecasts.
• Advances in the understanding of differ-
ences between the different models (i.e.
cloud, vapour-lapse and cryospheric feed-
backs).
• Improvements on temporal and spatial
resolutions, computational methods and
parameterization.
• Elimination of the use of flux adjust-
ments, although there are some biases
that remain among the different simula-
tions.
• Improved simulation of tropical cyclones.
• Exploration and production of ensembles
of model simulations.
• Incorporation of carbon cycle simulations
on some AOGCMs.
• Sensitivity experiments have been
improved through deeper evaluation of
Earth system models of intermediate
complexity.
Climate models analyse Earth processes
by using three-dimensional grid cells within
which mass and energy fluxes and storages
are quantified by a number of equations
describing the behaviour of several climatic
variables. The models provide numerical
solutions to the Navier Stokes equations
devised for simulating meso- to large-scale
atmospheric and oceanic dynamics, in
addition to parameterization schemes (i.e.
radiative transfer, turbulent mixing, bound-
ary layer processes, cumulus convection,
precipitation and gravity wave drag)
(Govindan et al., 2002). GCM simulations are
carried out by means of a large set of heavy
computations and thus require a considerable­
12 A. Jarvis et al.
amount of both processing capacity and time
to be able to produce a single prediction.
GCMs must be calibrated using past meas-
urements of climate variables and then fed a
set of boundary conditions (such as the
concentration of greenhouse gases (GHGs))
with which they simulate climate behaviour
at coarse spatial resolutions. However,
climate models are not perfect, mainly
because the current theoretical understand-
ing of climate is still incomplete and a range
of environmental and Earth processes still
remain uncertain, leading to simplification
and thus likely bias in predictions. Significant
improvements have been achieved since the
late 1990s and comprehensive evaluations of
climate models have yielded detailed conclu-
sions on which processes might be adequately
simulated and which models may simulate
better the different Earth processes involved
in climatic changes (Reichler et al., 2007).
There are marked differences between differ-
ent models, based on the selection of numer-
ical methods employed, the spatial resolution
of the simulation, and the subgrid-scale
parameters (IPCC, 2001, 2007; Govindan et
al., 2002; Reichler and Kim, 2008).
A climate model is a very complex system
in itself and the design of an evaluation
system with enough complexity to provide
clear conclusions on the main issues surround-
ing the possible model errors can be as compli-
cated as the model. GCMs are thus generally
tested at the system level by comparing only
the results of selected variables with their
observations. Such tests can reveal predictive
accuracy problems, but the source of those
problems is often hidden by the model’s
complexity, and, for this reason, comprehen-
sive evaluations take into account the compo-
nent level (i.e. isolating each process and
testing it one at a time) (IPCC, 2007). Due to
non-linearities in processes governing
climate, the climate system response to
perturbations depends to some extent on its
basic state (Spelman and Manabe, 1984).
Consequently, for models to predict future
climatic conditions reliably, they must simu-
late the current climatic state with some as
yet unknown degree of fidelity. Poor model-
ling skills in simulating present climate would
result in the misrepresentation of certain
physical or dynamical processes (Collins et al.,
2006; Delworth et al., 2006; IPCC, 2007).
The IPCC TAR reported that seven differ-
ent GCMs were used in the development of
climate change projections, while the IPCC
FAR reported projections from 21 different
GCMs (Table 2.1). These models have been
developed by different climate research
centres in different countries and have been
tested to different extents (IPCC, 2007; Chou
et al., 2008; Reichler and Kim, 2008; Pierce et
al., 2009; Zhou and Zhang, 2009). Model
performance varies according to the evalu-
ated criteria (e.g. variable, temporal coverage,
time slice, among others).
As changes in precipitation and in extreme
events are increasingly more complicated to
simulate than temperature changes, evalu-
ations have largely focused on evaluating
rainfall trends, especially within the tropics
(e.g. Timmermann et al., 1999; Neelin et al.,
2006; Hu and Zhou, 2007; Chou et al., 2008;
Pierce et al., 2009). The Coupled Model Inter­
comparison Project (CMIP) (Program for
Climate Model Diagnosis and Inter­
comparison, PCMDI) was created in the mid-
1990s with the aim of evaluating model
outputs of a large list of GCMs. CMIP-1
(Meehl et al., 2000) was the first phase of the
project and evaluated 18 GCM patterns
(Reichler and Kim, 2008), CMIP-2 (Covey et
al., 2003; Meehl et al., 2005a) evaluated 17
GCMs, and CMIP-3 (IPCC, 2007; PCMDI,
2007) evaluated 22 GCMs. Results of these
evaluations are available through the CMIP
project web page (CMIP, 2009). Evaluation of
accuracy among GCMs, however, is still not
representing the whole possible picture of
variability and thus does not fully describe
all sources of uncertainty regarding climate
change projections. Significant amounts of
effort continue to be levelled at GCM
evaluation­.
Special Report on Emissions Scenarios
(SRES)
Anthropogenic activities are the key drivers
of climatic change. Changes in atmospheric
concentrations of GHGs and aerosols, land
use and land cover change (LULCC), and solar
radiation from both natural and human
 Scenarios of Climate Change Within Agriculture 13

Table 2.1.  List of GCMs used in the Fourth Assessment Report (FAR).
Short name Model Atmospherea Oceana
MIRCH MIROC3.2. (hires), Japan T106, L56 0.28×0.19, L47
MIRCM MIROC3.2. (medres), Japan T42, L20 1.4×(0.5–1.4), L43
BCCRC BCCR-BCM2.0, Norway T63, L31 1.5×0.5, L35
C3T47 CGCM3.1 (T47), Canada T47 (3.75×3.75), L31 1.85×1.85, L29
C3T63 CGCM3.1 (T63), Canada T63 (2.8×2.8), L31 1.4×0.94, L29
CNRMC CNRM-CM3, France T63 (2.8×2.8), L45 1.875× (0.5–2), L31
CSIRO CSIRO-Mk3.0, Australia T63, L18 1.875×0.84, L31
GFD20 GFDL-CM2.0, USA 2.5×2.0, L24 1.0×(1/3–1), L50
GFD21 GFDL-CM2.1, USA 2.5×2.0, L24 1.0×(1/3–1), L50
GISSA GISS-AOM, USA 4×3, L12 4×3, L16
GISSH GISS-EH, USA 5×4, L20 5×4, L13
GISSR GISS-ER, USA 5×4, L20 5×4, L13
IAPFG IAP-FGOALS1.0-G, China 2.8×2.8, L26 1×1, L16
INMCM INM-CM3.0, Russia 5×4, L21 2.5×2, L33
IPSLC IPSL-CM4, France 2.5×3.75, L19 2× (1–2), L30
MPICM ECHAM5/MPI-OM, Germany T63, L32 1×1, L41
MRICM MRI CGCM2.3.2A, Japan T42, L30 2.5× (0.5–2.0)
NCARC NCAR-CCSM3, USA T85L26, 1.4×1.4 1×(0.27–1), L40
NCARP NCAR-PCM, USA T42 (2.8×2.8), L18 1×(0.27–1), L40
UKMOC UKMO-HadCM3, UK 3.75×2.5, L19 1.25×1.25, L20
UKMOG UKMO-HadGEM1, UK 1.875×1.25, L38 1.25×1.25, L20
INGVE INGV-SXG, Italy T42, L19 2×(0.5–2), L31
aHorizontal (T) resolution indicates number of cells into which the globe was divided. Vertical (L) resolution indicates the
number of layers into which the atmosphere or ocean was divided. When a model is developed with different latitudinal
and longitudinal resolutions, the respective cell sizes (Lon×Lat) in degrees are provided instead of a unique value.

processes lead to changes in Earth and
atmospheric processes by affecting the
absorption, scattering and emission of radia-
tion within the atmosphere and the Earth’s
surface (IPCC, 2007). Human activities result
in emissions of four long-lasting GHGs: CO2,
methane (CH4), nitrous oxide (N2O) and
halocarbons. Due to current intensification
and expansion of anthropogenic activities,
emissions of these gases have become far
larger than their respective removal
processes. The effect of human activities on
climate therefore directly depends on both
current and future emissions (IPCC, 2000,
2001, 2007; Arnell et al., 2004).
There is neither a global consensus on
what pathway the world should adopt in
terms of GHG emissions reductions, nor a
consensus with respect to the degree at which
emissions are currently affecting human
activities (especially agriculture). The estab-
lishment of multiple emission scenarios is
therefore necessary if the impacts of climatic
change are to be forecasted. Emission scenar-
ios are designed to represent a set of different­
GHG concentration storylines and different
politically oriented futures. In 1990, and
again in 1992, the IPCC developed the IS92
family of emission scenarios (Leggett et al.,
1992), which were subsequently widely used
to drive climate models and determine the
likely impacts of climate change. Each emis-
sion scenario corresponded to a particular
set of assumptions about future population
totals, economic development and LULCC.
However, the scenarios were not constructed
with impact assessments in mind and little
attempt was made by the impact assessment
community to ensure that the socio-economic
and demographic ‘worlds’ being impacted by
climate change were consistent with the
‘worlds’ used to construct the emissions
scenarios (Arnell et al., 2004). With this in
mind, by the mid-1990s, improvements in
the understanding of many of the processes
behind the emission of GHGs led to the
development of a new set of more adequate
scenarios called the ‘SRES scenarios’ (IPCC,
2000). In spite of the existence of scenarios,
however, the possibility that any single
14 A. Jarvis et al.
emissions­path will occur exactly as described
is highly uncertain (IPCC, 2000), mainly
because there is no way to assign them with
single probabilities of occurrence.
Four different SRES narrative storylines
were developed to describe the relationships
between emission driving forces and their
evolution. Each storyline represents different
demographic, social, economic, technological
and environmental developments. For each
storyline the IPCC developed, different
scenarios using different modelling
approaches and a total of 40 SRES scenarios,
housed in four major families of scenarios,
were developed (IPCC, 2000). The four fami-
lies of SRES storylines represent world futures
in two dimensions: a focus on economic or
environmental concerns, and global or
regional development patterns (IPCC, 2000;
Arnell et al., 2004; Fig. 2.1). Detailed informa-
tion on SRES scenarios development and
modelling is available in the IPCC Special
Report on Emissions Scenarios (IPCC, 2000).
The families of scenarios are based on
three main driving forces: (i) demographic
change; (ii) social and economic develop-
ment; and (iii) the rate and direction of tech-
nological change. In short, the four families
of emissions scenarios can be described as:
A1: Very rapid economic growth, global
population that peaks in mid-century
and declines thereafter, and the rapid
introduction of new and more efficient
technologies. Major underlying themes
are: convergence among regions, capac-
ity building, and increased cultural and
social interactions, with a substantial
reduction in regional differences in per
capita income. The A1 family splits into
three groups that describe alternative
directions of technological change in
the energy system. The three A1 groups
are distinguished by their technological
emphasis: fossil intensive (A1FI), non-
fossil energy sources (A1T), or a balance
across all sources (A1B).
A2: Heterogeneous world. The underlying
theme is self-reliance and preservation
of local identities. Fertility patterns
across regions converge very slowly
resulting in a continuously increasing
Global
Governance
A1 B1
Environmental
Economic
Development Development
Governance
A2 B2
Local
Fig. 2.1.  SRES storylines (adapted from Arnell et
al., 2004).
global population. Economic develop-
ment is primarily regionally oriented and
per capita economic growth and techno-
logical change are more fragmented and
slower than in other storylines.
B1: A convergent world with the same
global population as in the A1 storyline,
but with rapid changes in economic
structures towards a service and infor-
mation economy with reductions in
material intensity and the introduction
of clean and resource-efficient technolo-
gies. The emphasis is on global solutions
to eco­nomic, social and environmental
sustainability, including improved
equity, but without additional climate-
harming development.
B2: Emphasis on local solutions to
economic, social and environmental
sustainability. It is a world with contin-
uously increasing global population at a
rate lower than A2, intermediate levels
of economic development, and less
rapid and more diverse technological
change than in the B1 and A1 storylines.
While the scenario is oriented towards
environmental protection and social
equity, it also focuses on local- and
regional-level development processes.
The SRES scenarios project an increase of
baseline global GHG emissions by a range of
 Scenarios of Climate Change Within Agriculture 15
9.7–36.7 GtCO2-eq (25–90%) between 2000
and 2030 (Fig. 2.2). The rate of increase of
emissions of CO2 are relatively constant for
the two families of scenarios (A2 and B2),
while other scenarios show a peak and then a
decrease in CO2 emissions. Scenarios B1, A1B
and A1T show their peak in 2050 with CO2
emissions up to 45, 70 and 50 GtCO2-eq,
respectively, while the scenario A1FI shows a
peak in 2080 with approximately 130
GtCO2-eq.
Uncertainties in climate predictions
Uncertainty is a significant issue arising
from any climate change projection (Carter
et al., 2001; Arnell et al., 2004) as everything
within the context of climate change is
merely a forecast. This uncertainty arises
from three main sources: (i) uncertainty in
forcing scenarios (see earlier section on
GCMs); (ii) uncertainty in modelled
responses to given forcing scenarios; and
(iii) uncertainty due to missing or misrepre-
sented physical processes by models.
Perhaps the most important single source
of uncertainty when forecasting future
climates relates to the changes in GHG
Scenarios
A1B
25
A1T
A1FI
A2
20 B1
B2
IS92a
15
10
2000 2020
Fig. 2.2.  Anthropogenic emissions of CO2 for the six illustrative SRES scenarios, A1B, A2, B1, B2, A1FI
and A1T. For comparison the IS92a is also shown (adapted from IPCC, 2000, 2001).
emissions­(Quiggin, 2008). The relationship
between climate change and uncertainty
about emissions is complicated by the fact
that the policy changes that will help to
determine future growth in emissions are
themselves a response to projections of
future climate (Quiggin, 2008) – so the
process tends to be replicative and redun-
dant. The extent to which mitigation meas-
ures are required in order to maintain
agricultural production depend on the accu-
racy of climate forecasts, and climate fore-
casts directly depend on changes in
atmospheric concentrations of GHGs, which
are driven by mitigation strategies.
Projections of future socio-economic condi-
tions under a given storyline are uncertain
(Carter et al., 2001). Population projections
for a storyline, for example, depend on
assumed fertility and mortality rates and,
like climate projections, become increasingly
uncertain further into the future.
Downscaling from a world view to a country
view, and to regions within a country, adds
even more uncertainty. Projected future GDP
for a storyline is even more uncertain,
because it depends on: (i) specific economic
assumptions made about growth and the
2040 2060 2080 2100
Year
16 A. Jarvis et al.
implementation of technological changes;
(ii) the characteristics of the economic model
used to project GDP; and (iii) assumptions
about future exchange rates. Models, there-
fore, need to be calibrated to each different
forcing scenario and this calibration involves
further uncertainty in the analysis. Under a
global commitment to cap CO2 emissions, in
order to maintain temperature rises below
2°C, the degree of uncertainty regarding
GHG emission scenarios would be substan-
tially reduced.
Assumptions on economic and popula-
tion growth driving the generation of differ-
ent scenarios are not the only source of
uncertainty. Application of climate models
to boundary conditions established by emis-
sion scenarios also introduces uncertainty.
However, the degree of uncertainty among
models and model-ensembles can be calcu-
lated so that we know both the likely future
climates and the likelihood of producing a
wrong estimate (Thorpe, 2005). This is
because modelled responses by different
GCMs produce uncertainty mainly due to
the fact that each model uses a different set
of equations in order to quantify the degree
at which the atmospheric processes are
affected by changing concentrations of
GHGs. These different equations have the
general characteristic of responding to
increases in CO2 concentrations with
increases in temperatures, but responses in
precipitation and other weather variables
may differ significantly from one model to
another. The use of multi-model mean
ensembles (IPCC, 2001, 2007) permits the
reduction and quantification of uncertainty,
but is still affected by performance of indi-
vidual members (IPCC, 2001, 2007;
Stainforth et al., 2005; Thorpe, 2005;
Quiggin, 2008; Nychka et al., 2009).
Selection of the best ensemble members is
thus required if accurate forecasts are to be
produced.
Future climate projections are the result
of the application of a numerical weather
model, which often tends to misrepresent
atmospheric processes. There are two
reasons for this: first, because, a truncation
error is utilized for the numerical method,
and secondly, because patterns occurring at
smaller scales than the grid resolution must
be included (i.e. parameterization) (Thorpe,
2005; Quiggin, 2008). Structural uncer-
tainty is introduced by scientific choices of
model design and development (Nychka et
al., 2009), including model parameteriza-
tion, equation and choice of cell size. There
are a large number of choices in construct-
ing a complex model such as a GCM, and
inevitably, these choices lead to different
results (Quiggin, 2008). Current models
attempt to include the dominant physical
processes that govern the behaviour and the
response of the climate system to specified
forcing scenarios, but representing all phys-
ical processes results in a very difficult task.
For that reason, models need to be cali-
brated by using past measurements of
climates. Confidence in a model can be
gained through simulations of the historical
record or of palaeoclimate, but such oppor-
tunities are much more limited than those
available through weather prediction.
There is still a wide range of sources of
uncertainty, such as the influence of various
forcings on global warming (i.e. solar output
changes, aerosol concentration), feedback
processes that would produce additional
CO2 emissions (e.g. bush fires), cost–benefit
uncertainty on adaptation and mitigation
measures (especially relevant in the case of
developing countries), and fabricated uncer-
tainty (politically convenient uncertainty)
(Quiggin, 2008).
Regional climate models (RCMs) and
seasonal forecasting
Assessing future projections of climates
driven by the different changes of concen-
trations of GHGs, anthropogenic activities,
natural forces, and other boundary and
initial conditions through a GCM requires a
large storage and processing capacity and,
due to that, temporal and spatial resolutions
of GCM outputs are still limited. Agricultural
landscapes vary on a small scale and broad
resolution results of GCMs do not provide
the necessary spatial accuracy in order to
assess the likely impacts of climate change
 2020–2029 2090–2099

Plate 1. Projected surface temperature changes for the early and late 21st century relative to the period 1980–
1999. Values show the atmosphere–ocean general circulation model (AOGCM) multi-model average projections
(OC) for the B1 (top), A1B (middle) and A2 (bottom) Special Report on Emissions Scenarios (SRES) scenarios
averaged over the decades 2020–2029 (left) and 2090–2099 (right). As shown in figure TS.28 (p. 72) of the IPCC
(2007) Fourth Assessment Report, Technical Summary.
 (mm/day)

Plate 2. Multi-model mean changes in precipitation (mm/day). To indicate consistency in the sign of change, regions are stippled where at least 80% of models agree on
the sign of the mean change. Changes are annual means for the Special Report on Emissions Scenarios (SRES) A1B scenario for the period 2080–2099 relative to
1980–1999. As shown in figure 10.12 (p. 769) of the IPCC (2007) Fourth Assessment Report, Chapter 10 (Global Climate Projections), Report of Working Group I of the
IPCC, Climate Change 2007: The Physical Science Basis.
 Scenarios of Climate Change Within Agriculture 17
on agricultural production. Downscaling is
therefore often needed in order to provide
higher resolution future climate forecasts.
Regional climate modelling (also known as
dynamic downscaling) is the most numer-
ically and climatologically stable (and
accepted) approach when forecasting climatic
changes at finer (i.e. regional) resolutions.
RCMs are based on similar physical relations
to GCMs, but applied on high resolution
(typically 20–50 km) grid cells and within a
limited domain (typically 5000 × 5000 km2).
They are forced at their lateral boundaries by
the output of the GCMs (Giorgi, 1990;
McFarlane et al., 1992; Giorgi et al., 1993a,
b, 1994; Caya et al., 1998; Lenderink et al.,
2007) in order to produce forecasts at
regional scales.
Since RCMs are based on physics they can,
at least in principle, represent the complex
interactions and feedbacks involved with
climate change. However, like GCMs, they
may contain systematic errors leading to
uncertainties and they are computationally
expensive. Because it is impossible to regu-
larly perform high-resolution integrations of
GCMs at high resolutions, it is possible to
nest a high-resolution model inside a low-
resolution GCM (Dickinson et al., 1989;
Giorgi 1990; Giorgi and Marinucci, 1991).
The nested modelling technique consists of
using coarse resolution GCM to carry out
simulations of global climate and then
employing the GCM output to drive a high
resolution limited area model (LAM) over an
area of interest. The basic idea is that the
GCM can provide the correct large-scale circu-
lation response to global climatic forcings,
and the LAM can describe the effect of sub-
GCM grid-scale forcings, due for example to
large water bodies, surface vegetation charac-
teristics, or complex topography and coast-
lines that may significantly influence the
characteristics of local climates (Dickinson et
al., 1989; Giorgi, 1990).
Regional climate modelling adds two
types of small-scale information to GCM
results. First, it adds information on the
local conditions at specific locations. This is
typically important when large horizontal
gradients occur. Secondly, it adds informa-
tion on processes that are small scale but
which are not necessarily tied to a specific
location, like for example frontal systems,
small-scale convective precipitation, and
other meso-scale phenomena (Lenderink et
al., 2007). RCM forecasts are, however, more
uncertain than GCM projections of future
climates. RCMs are themselves models, and
in addition to that, base their modelling
approach in the outputs of another model
(i.e. the GCM). The spread (i.e. variance)
between RCM outputs driven by different
boundary conditions is small in comparison
to the potential variance when applying a
GCM among different boundary conditions
(i.e. predictions within different emission
scenarios may not differ significantly)
(Déqué et al., 2007; Lenderink et al., 2007).
However, changes in parameterization of
RCMs may strongly impact on the extremes
(e.g. daily temperature extremes) (Kjellström
et al., 2007). RCM results cannot thus be
used directly to produce scenarios that
represent the range of outcomes based on
the GCM knowledge, mainly because GCM
and RCM outputs for a single region may
differ significantly in both accuracy and vari-
ance. The variance arising from a GCM comes
from the numerical approximation to the
climate system and the boundary conditions
used to run the model; however, variance in
RCMs may arise only from the different
representation of small-scale physics, which
may lead to propagative errors in the fore-
casting (MacCracken et al., 2004; Lenderink
et al., 2007).
The evaluation of the quality and useful-
ness of climate modelling systems is depend-
ent upon an assessment of both the limited
predictability of the climate system and the
uncertainties stemming from model formu-
lation. One means of assessing the perform-
ance of an RCM examines its ability to
represent the natural inter-annual variability
on monthly and seasonal timescales. While
ensemble experiments demonstrate that the
predictability of the regional climate varies
strongly between different seasons and
regions, important sensitivities of the model-
ling system to parameterization choices
might remain uncovered. In particular,
compensating mechanisms related to the
long-term representation of the water cycle
18 A. Jarvis et al.
are revealed as a result of unrealistic cloud-
radiative feedbacks (Vidale et al., 2003).
RCMs have suffered from a lack of
comprehensive assessment of their accuracy,
due to their difficult access to non-climatic
research centres, and the lack of global
published data for different models, time
slices and climatic variables. Despite that,
regional impacts of climate change on agri-
cultural production have also been assessed
via RCMs (Guereña et al., 2001; Kueppers et
al., 2005; Blenkinsop and Fowler, 2007; Yano
et al., 2007; Solman et al., 2008; Nuñez et al.,
2009).
Predicted changes in temperature
The FAR of the IPCC (2007) describes
changes in temperature at different levels of
the atmosphere. We will focus only on near-
to-surface changes on land as those changes
directly influence agricultural production.
Results of different GCMs indicate that in
both the TAR and the FAR (IPCC, 2001,
2007) global temperatures are to increase.
Land and sea surface temperatures will
increase at rates never experienced before,
and, depending on the emission scenario,
these changes are reversible to a certain
extent. Warming over sea is predicted to be
considerably lower than warming over land
areas across all latitudes except below the
43°S and above the 70°N latitudes.
The FAR AOGCM ensemble (Plate 1)
provides the most sophisticated set of
models in terms of the range of processes
included and consequent realism of the
simulations compared to observations
(IPCC, 2007). On average, this ensemble
projects an increase in global mean surface
air temperature of 1.8°C, 2.8°C and 3.4°C in
the B1, A1B and A2 scenarios, respectively,
by 2090–2099 relative to the 1980–1999
baseline (IPCC, 2007). There is a range of
variation among different models and
according to the different geographic areas.
In general, agricultural production will be
highly impacted if temperature changes go
above 2°C (IPCC, 2007; Brown and Funk,
2008; Lobell et al., 2008), and in most of the
tropical zones temperatures are likely to
increase between 1.4 and 5.8°C in a medium-
range scenario (A1B) by the end of the
century. In fact, in a medium-range scenario
such as the A1B, a 2°C temperature increase
would occur in most geographic areas by the
2050s, and in a high-estimate scenario such
as A2, this threshold is far exceeded in the
2020 decade in most geographic areas (IPCC,
2001, 2007). High latitudes and altitudes
hold the greatest increments, while low-
lying and flat areas show the lowest esti-
mates. Uncertainty in temperature
projections is relatively low, as all models
predict global warming (IPCC, 2007).
Changes in temperatures for Africa are
stronger in the Sahel belt than in southern
sub-Saharan Africa. Under the A1B scenario,
Central Africa receives the least increments
in annual mean temperatures, and also in
the December–February (DJF) and June–
August (JJA) periods. Temperatures in JJA
will be markedly more affected than those of
DJF and are also above the annual average.
The largest temperature responses in North
Africa are projected to occur in JJA, while
the largest responses in southern Africa
occur in September–November (SON). The
seasonal structure of temperature responses,
however, is modest compared with extra
tropical regions (IPCC, 2007). The average
increase in global mean temperatures is
1.6°C and 8.4°C by the 2020s and 2050s,
respectively, under the A2 emission scenario
(business as usual). There is no significant
variation in diurnal temperature ranges in
the 2020 decade; however, a likely increase
from 11.2 to 12.24°C is expected by the
2050s. Cold periods present more significant
temperature increases (i.e. 10.2°C increase in
the coldest quarter by 2050s) with respect to
warm periods (i.e. +6.4°C by 2050s).
Northern latitude countries show greater
increments in temperatures derived from
changing climates. Under the A1B emission
scenario, temperatures in Europe would
increase more than 2°C by the 2020 decade
and by more than 3°C in 2050. The same
occurs with North America and Siberia. Asia
is the region with most diverse changes (i.e.
high spatial variation) due to the combina-
tion of tropical and subtropical conditions.
In the JJA period, however, temperature
 Scenarios of Climate Change Within Agriculture 19
changes in northern latitudes are not consid-
erably high. Southern latitudes in Latin
America show the least temperature
increases, with all models predicting changes
below 1.5°C by 2020, below 2°C by 2050 and
below 4°C by 2100 under the A1B emission
scenario. Differences between models
increase towards the future, meaning that
impact studies of climate change on agricul-
tural production should be focused on short-
and mid-term forecasts.
Individual models of the ensemble
perform relatively well in comparison to
multi-model ensembles. Warming trends in
the NCAR (National Center for Atmospheric
Research) models PCM (Parallel Climate
Model) and CCSM3 (Community Climate
System Model version 3) show that even if
all CO2 emissions were stopped, global
temperatures would increase between 0.4
and 0.6°C by 2100. At the end of the 21st
century, warming in the low-estimate
climate change scenario (SRES-B1) is 1.1°C
and 1.5°C in the PCM and CCSM3 models,
respectively, with sea level rising to 13 and
18 cm above 1999 levels (Meehl et al.,
2005b). A medium range scenario (SRES-
A1B) produces a warming at the end of the
21st century of 1.9°C and 2.6°C, with about
18 and 25 cm of sea level rise in the two
models. For the high estimate scenario (A2),
warming at 2100 is about 2.2°C and 3.5°C,
and sea level rise is 19 and 30 cm. If concen-
trations of GHGs and other atmospheric
constituents in NCAR’s simulations are held
fixed at 2100 values, an additional 0.1–0.3°C
of temperature rise would be expected under
the B1 scenario by 2200 and an additional
0.1°C by 2300.
Predicted shifts in rainfall patterns
Projections of precipitation changes differ
significantly from temperature projections
as they are driven by a wider range of atmos-
pheric processes and thus present a greater
dependence on the mechanics of the GCM
used to forecast, thus leading to greater
uncertainty in predictions. Rainfed agricul-
ture depends heavily on rainfall patterns,
and precipitation changes may lead to severe
droughts in some places and waterlogging in
others. There could be some cases in which
agriculture may be favoured by increases in
rainfall, or cases in which low-cost changes
or simple adjustments to the farming system
are required (Lobell et al., 2008).
Northern latitudes and highlands in the
tropics show the highest confidence in
projections (Plate 2) as the mechanics with
which most of the GCMs work tend to esti-
mate relatively similar patterns in precipi-
tation in such areas. Increases in rainfall
over the tropics are generally driven by high
certainty, while decreases seem to present a
greater degree of variance among the model
ensemble members. Central America and
the Caribbean islands show significantly
decreasing rainfall patterns, as well as a shift
in variance throughout the year (IPCC,
2007). Most areas in sub-Saharan Africa and
Latin America, as well as Australia and the
whole Indian subcontinent, suffer a high
degree of uncertainty, indicating the need
for improved forecasts or analyses that are
more short term for these areas. Under the
A2 emission scenario, a global increase of
1.9% in total annual rainfall is expected by
the 2020s, and a more severe increase
(22.8%) is expected by 2050s. Dry and wet
periods in both the 2020s and the 2050s get
wetter, but there’s a greater relative gain on
dry periods, indicating a smaller difference
between dry and wet periods, which could
lead to changes in crop phenology and thus
planning of harvests.
In Africa, a 20% drying in the annual
mean is typical along the African
Mediterranean coast (A1B) by the end of the
21st century. Drying is seen throughout the
year and is predicted by almost every model.
The drying signal extends into the Sahara,
and down the west coast as far as 15°N. The
processes include increased moisture diver-
gence and a systematic poleward shift of the
storm tracks affecting the winter rains, with
positive feedback from decreasing soil mois-
ture in summer (IPCC, 2007). In southern
Africa, a similar set of processes produces
drying that is specifically robust in the
extreme south-west winter, a manifestation
of a much broader-scale poleward shift in
the circulation across the South Atlantic and
20 A. Jarvis et al.
Indian Oceans. In Europe, the annual area-
change up to the 2080s varies from 0 to 16%
in northern Europe, and from ­–4 to –27% in
southern and central Europe. In summer,
however, projected changes vary in sign
among models. Most land areas in northern
latitudes (i.e. North America and Asia) have
the same trend in terms of certainty: north-
ern zones with significant increases in rain-
fall show the greatest certainty (with 80% or
more models agreeing), while areas nearer
to the tropics show drying trends with low
certainty.
Seasonal changes are also different among
regions. Rainfall pattern changes in Asia
show spatially differentiated drying trends
over the whole area. The Middle East shows
a significant decrease (between –5 and 20%),
and considerably lower certainty (less than
50% of the models agreeing) in overall
annual precipitation, as well as in the differ-
ent seasons, with more marked decreases in
the JJA season. Increases are forecast in
north Asia and Russia with high certainty
(A1B emission scenario). Latin America is a
zone in which particularly high differences
among GCM patterns are observed.
Predictions show severe drying patterns in
the Amazon basin during the JJA season,
and significant increases in precipitation
throughout the year on the Pacific coast of
Colombia, Ecuador and Peru.
Changes in extreme events
Regional models are most suitable to evalu-
ate the likelihood of changes in extreme
events, and while they have been widely
applied in Europe and North America, other
areas such as Africa, Latin America and some
parts of Asia mainly depend on GCM projec-
tions, and detailed regional analyses are still
limited in number (Solman et al., 2008;
Nuñez et al., 2009). However, climate change
will certainly influence the frequency and
intensity of drought and waterlogging
(Timmermann et al., 1999; IPCC, 2001, 2007;
Ekström et al., 2005; Fowler et al., 2005;
Blenkinsop and Fowler, 2007). Regional
models also suggest that rainfall intensity is
to increase over southern Africa (Tadross et
al., 2005; IPCC, 2007). Compensation
between intensity and frequency of rain is
expected when the total annual rainfall tends
to be maintained over time (i.e. more intense
rainfall events spread throughout the year).
In almost all global land areas, warm seasons
will probably be extremely warm by the end
of the 21st century, with very high confi-
dence under the A1B scenario (IPCC, 2007),
with increases in the wet season rainfall
intensity as well, due mainly to increased
cloud loadings and surface evaporation
(IPCC, 2007).
The degree to which changes in atmos-
pheric processes led by changes in concen-
trations of GHGs influences the likelihood
or frequency of extreme storms is still not
known. Hurricanes generally occur over the
oceans in regions where sea surface temper-
atures exceed a certain threshold (Trenberth,
2005). There is a non-linear upward trend in
sea surface temperatures over the 20th
century. This trend is most pronounced in
the past 35 years in the extra-tropical North
Atlantic (Trenberth, 2005), and will be likely
to continue during the whole of the 21st
century. It is associated with global warming
and has been attributed to human activity
(IPCC, 2001, 2007). In the tropical North
Atlantic (the region of most relevance to
hurricane formation), multi-decadal vari-
ability dominates sea surface temperatures,
leading to different temporal patterns of
hurricane formation (Trenberth, 2005).
However, there is no sound theoretical basis
for drawing any conclusions about how
anthropogenic climate change affects hurri-
cane numbers or tracks (Vecchi et al., 2008).
Some model results suggest a shift in hurri-
cane intensities towards stronger hurricanes
(Knutson and Tuleya, 2004; Elsner et al.,
2008), while others indicate a likely drop in
hurricane frequency (Knutson et al., 2008).
The ENSO phenomenon is the strongest
natural inter-annual climate fluctuation
across the globe. ENSO originates in the
tropical Pacific Ocean and has large effects
on the ecology of the region. It can be under-
stood as an irregular low-frequency oscilla-
tion between a warm (El Niño) and a cold
(La Niña) state (Timmermann and Menviel,
2009). Recent changes in frequencies and
 Scenarios of Climate Change Within Agriculture 21

intensities of ENSO, especially regarding a
perceptible increase in El Niños, suggest
that anthropogenic activities could have
influenced these changes. This has been
addressed via several GCMs, but the inabil-
ity of the models to fully simulate ENSO has
been debated (Timmermann et al., 1999).
Whether the frequency and/or intensity of
El Niños will increase with human-led
climate change is still not known.
Sea level rise
As temperatures increase, seawater expands
in volume and increases in level (thermal
expansion). Temperature increases also
contribute to glaciers and ice caps melting.
The IPCC (2007) estimated that under an
intermediate emission scenario (A1B), ther-
mal expansion would produce between 0.3
and 0.8 m of sea level rise by 2300. This is
mainly due to the fact that energy moves
slowly from the surface to the deep parts of
the ocean (IPCC, 2007). Understanding of
sea level rises is still limited, mainly due to
the understanding of the many different
processes from which sea level rise is driven.
Uncertainty is relatively high, and future
projections (Fig. 2.3) range from 20 to 50 cm
to 2050, depending on the emission scenario.
Under the B1 scenario (the best case
scenario), the likely changes in sea level
range between 18 and 38 cm, while in the
worst case scenario (A1FI), the likely change
could range from 26 to 59 cm by the end of
the 21st century (IPCC, 2007).
Though temperature increases show signs
of levelling off 100 years after stabilization,
sea level continues to rise unabated with
proportionately much greater increases
compared to temperature (i.e. NCAR models)
(Meehl et al., 2005b). This trend is also
observed for other GCMs (IPCC, 2007).
Thus, even if GHG emissions could be
stabilized, sea level rise is likely to continue

500 Estimates Instrumental record Projections

of the past of the future
400
Sea level change (mm)

300

200

100

–100

–200

1800 1850 1900 1950 2000 2050 2100

Year

Fig. 2.3.  Time series of global mean sea level (deviation from the 1980–1999 mean) in the past and as
projected for the future. For the period before 1870, global measurements of sea level are not available.
The grey shading (left pane) shows the uncertainty in the estimated long-term rate of sea level change in
the past. The line (middle pane, left) is a reconstruction of global mean sea level from tide gauges and
the shading around the line denotes the range of variations from a smooth curve. The short line (middle
pane, right) shows global mean sea level observed from satellite altimetry. The shading (left pane)
represents the range of model projections for the SRES A1B scenario for the 21st century, relative to the
1980–1999 mean, and has been calculated independently from the observations (adapted from IPCC,
2007).
22 A. Jarvis et al.
to have an impact for centuries to come.
Flooding of coastal lands could therefore be
a significant impact of sea level rise, in
addition to salinization of soils and subsur-
face water in coastal regions. Nicholls (2002)
estimates that 16–388 million people will
experience flooding with a 55 cm sea level
rise, with this figure rising to 510 million
people under a 96 cm rise.
Impacts of Climate Change on
Agriculture
The impacts of climate change on agriculture
are expected to be widespread across the
globe, although studies suggest that African
agriculture is likely to be most affected due to
heavy reliance on low-input rainfed agricul-
ture and due to its low adaptive capacity
(Mertz et al., 2009). Broadly speaking,
climate change is likely to impact crop
productivity directly through changes in the
growing environment, but also indirectly
through shifts in the geography and preva-
lence of agricultural pests and diseases, asso-
ciated impacts on soil fertility and biological
function, and associated agricultural biodi-
versity. While many impact predictions tend
towards the negative, increased CO2 will also
contribute to enhanced fertilization –
although there is significant debate as to the
extent to which this may increase plant
growth. This section looks at these issues,
concentrating entirely on the expected
biophysical impacts. The resultant impacts
on food security, economics and livelihoods
are dealt with by Lobell and Burke (Chapter
3, this volume), and possible adaptation
options to confront the biophysical impacts
are dealt with in subsequent chapters.
Impacts on crop yields
IPCC (2007) concluded that ‘in mid- to high-
latitude regions, moderate warming benefits
crop and pasture yields, but even slight warm-
ing decreases yields in seasonally dry and
low-latitude regions (medium confidence)’. In
IPCC language, moderate warming is in the
range of 1–3°C. Smallholder and subsistence
farmers, pastoralists and artisanal fisher-folk
will suffer complex, localized impacts of
climate change (high confidence). Food and
forestry trades are projected to increase in
response to climate change with increased
dependence on food imports for most devel-
oping countries (medium to low confidence).
The report further concluded that warming
beyond 2–3°C was likely to result in yield
declines in all areas. This analysis was based
on a synthesis of 69 studies, which was a vast
improvement on the handful of studies used
in the TAR (IPCC, 2001). But even since the
IPCC FAR (2007) there has been a much larger
number of studies which examine the impacts
of climate change on crop production and
yields, including global multi-crop studies,
down to regional and national studies on
individual crops. This chapter summarizes
the IPCC findings, and provides a more
detailed analysis of impact studies arising
from 2006 to 2009.
There are fairly consistent pictures drawn
by different studies that show the potential
effects of changing climates (Rosenzweig et
al., 1995; Parry et al., 1999; Fischer et al.,
2002; Hitz and Smith, 2004; Lobell et al.,
2008). These all show steeply increasing
trends in adverse impacts, particularly in food
insecure regions among the tropics, which are
likely to increase the extent to which these
regions are food insecure, especially taking
into account that most of these regions
present the least adaptive capacity. Grain
yields are expected to fall in developing coun-
tries; however, the opposite is likely to happen
in developed countries (Crosson, 1997;
Fischer et al., 2001; IPCC, 2007). Geographies
of changes may influence yield responses: in
high latitudes (where most of the developed
countries are located), increased tempera-
tures could increase the duration of growing
seasons, thus benefiting farmers. However,
in developing countries, which are mostly
located in the tropics, this effect would not be
observed. Investment capacity within the
different agricultural sectors needs to be
considered if yield losses are to be offset
(Crosson, 1997). Moreover, yield reductions
will certainly result in increases in prices of
agricultural goods (Rosenzweig and Parry,
1994), and this impact will be greater for food
insecure regions.
 Scenarios of Climate Change Within Agriculture 23
Making sense of the results is a challenge
thanks to different GCM models being used
under different emissions scenarios with
different time frames (2030 through to
2100), and most importantly, through differ-
ent crop modelling approaches. We divide
this section up into three broad modelling
approaches to report on the likely impacts of
climate change on agricultural production:
empirical-based studies, mechanistic crop
modelling approaches, and niche-based
approaches. Further discussion on the
impacts of climate change on agricultural
production is also addressed briefly by Lobell
and Burke (Chapter 3, this volume).
Empirical approaches
Empirical approaches to evaluate the impacts
of climate change on crop production use
the past as the key to the future through
national and sub-national production data-
bases coupled with past climatic trends.
Some studies also make use of multi-site
experimental trial data. The studies
summarized in this section are just a small
subset of studies that have used empirical
approaches, but are presented to illustrate
the approach. Lobell et al. (2008) performed
a global analysis of likely impacts of climate
change on a range of crops, using past
production data to develop regressions
between climate conditions and agricultural
production. Linking to 18 GCM predictions
for the A2A scenario (an A2 sub-scenario)
for 2030, they predict significant yield
decreases on average, but significant varia-
bility in impacts between crops and for
different regions. They highlight South Asian
wheat, South-east Asian rice and southern
African maize as crop regions of particular
concern. Schlenker and Roberts (2006) used
historical agricultural production data for
the USA to determine that rising tempera-
tures from climate change may impact
maize- and soybean-growing environments
in the USA, but that negative impacts will be
likely to be observed with temperatures
above 29°C, and with precipitation either
above 790 mm or below 640 mm. For cotton
(a more heat-resistant crop) the temperature
threshold extends to 33°C. Schlenker and
Roberts also conclude that current maize
varieties in the USA will present low resist-
ance to changing conditions (i.e. low adapta-
tion potential), and that technological
options must be developed in order to sustain
production. Maize yields in the USA will be
likely to decrease by 29% to 2030 and by 46%
to 2080 if the B1 scenario storyline is to be
followed, with changes in temperature being
more important than changes in precipita-
tion, and with northern areas benefiting
from temperature increases. Soybean and
cotton production will also be affected, with
decreases in yields ranging from 16–21% by
the 2030s and 33–72% by the 2080s for
soybean, and between 18–19% by the 2030s
and 25–78% by the 2080s for cotton.
Mechanistic crop modelling approaches
These approaches make use of mechanistic
crop models such as the computer models
Decision Support System for Agrotechnology
Transfer (dssat), Erosion Productivity
Impact Calculator (epic) or the General
Large Area Model (glam), among others, to
examine the changes in crop productivity
under scenarios of global change. These
models are available for crops for which
there is explicit physiological knowledge.
Among the benefits of these approaches is
the fact that genetic parameters for specific
varieties can be incorporated into the
scenario analysis, in addition to manage-
ment practices. This provides a much greater
level of detail in assessing impacts, and the
evaluation of specific scenarios for adapting
to climate change. However, the high degree
of parameterization of mechanistic crop
models make their application at the global
level quite complex (Hansen and Jones,
2000), and requires a number of general
assumptions about on-farm management
and varietal selection. A detailed review of
methodological issues surrounding the use
of mechanistic simulation models for
predicting crop response to climate change
is provided by Challinor et al. (2009).
Brown and Rosenberg (1999) use the epic
model to show that wheat and maize yields in
the USA are unlikely to reduce their potential
24 A. Jarvis et al.
production by more than 10% if temperatures
rise by only 1°C (likely to occur during the
2020s). When temperature increases go
beyond 2.5°C (likely during the 2050s), they
predict sharp losses in productivity in both
crops, and when temperatures increase up to
5°C (i.e. the end of the 21st century), yield
losses start becoming severe, with decreases
from 13 to 75%. For maize in Africa and Latin
America, Jones and Thornton (2003)
predicted 10% reductions in yield to 2055,
but considerable spatial variability with a
mosaic pattern of regions with increases and
decreases across both continents. Similarly,
Erda et al. (2005) predict up to 37% reduction
in yields for rice, wheat and maize in China.
Aggarwal (2008) showed that India could lose
4–5 million t of wheat (5–7% of total wheat
production) with every temperature rise of
1°C, even after considering carbon fertiliz-
ation but no adaptation benefits. Challinor et
al. (2007) use the glam model for annual
crops to predict that groundnut yields in India
could drop up to 70%, but show that this
depends on the genotypic responses and
management practices in the face of adapta-
tion as well as on the water availability (i.e.
changes in rainfall). Extreme temperatures
are an important determinant of yield in
annual crops, specifically in parts of northern
and southern India. Changes in mean
temperature and their impact on develop-
ment rates, however, could be more relevant
than heat stress produced by extreme
temperature events in some periods of the
year, but this depends on the response of the
different genotypes. Genotypic adaptation is
thus important to respond adequately to
climate change in vulnerable environments,
as most of the responses in terms of yield
losses depend both on geography and on
genotypic responses. Challinor et al. also
report that even when optimal temperatures
are exceeded, the resulting increase in
duration of the growing period could mitigate
or even counteract the negative impacts of
passing reproductive temperature thresholds
on yield; however, there should also be enough
water to supply the crop’s extended growing
season. Sensitivity of genotypes might be a
key determinant when extreme events
become more frequent and more intense, and
this also influences the inter-annual vari-
ability of the crop’s yield (Challinor and
Wheeler, 2008).
Impacts of climate change on yields are
driven by the response of the crop to mean
temperature and mean temperature alter-
ations, the physiological response of the
crop to increased CO2 concentrations, the
interaction between water stress and CO2,
and the interactions between the different
variables and their respective changes and
change rates with the crop (Challinor et al.,
2009). However, considerable attention has
been paid to the evaluation of yield responses
under changing climates, even if current
mechanistic models are not widely accepted
and have not yet been proven to accurately
model current responses of crops to envir-
onmental conditions.
Niche-based approaches
Niche-based approaches (also referred to as
agroecological zoning approaches) generally
take a simpler view of crop adaptation, and
are especially useful for examining the
impacts of climate change on crops when
there is reduced physiological knowledge,
such as is the case for many minor crops.
Niche-based models use broad climatic
parameters of crop adaptation, and locate
those ‘niches’ under current conditions and
into the future through coupling with GCM
predictions. Two studies have taken this
approach to examine the global-scale impacts
of climate change on a range of crops. Fischer
et al. (2001, 2002, 2005) use a global agro-
ecological assessment and depict more than
three-quarters of the global land surface as
unsuitable for rainfed crop cultivation,
suffering severe constraints or being too
cold (13%), too dry (27%), too steep (12%),
or having poor soils (40%). They show that
under climate change, mixed and geographi-
cally varying impacts will be observed on
crop production. Developed countries
substantially gain production potential,
while many developing countries lose. At the
global level, however, enough food could be
produced on currently cultivated land if
sustainable management and adequate
inputs are applied (Fischer et al., 2002).
 Scenarios of Climate Change Within Agriculture 25
However, attaining this situation will require
substantial improvement of socio-economic
conditions in many developing countries to
enable access to inputs and technology
(Fischer et al., 2002). Lane and Jarvis (2007)
used the Ecocrop model on 41 important
crops, and using the HADCM3 GCM and the
A2A SRES emissions scenario showed how
the geography of agriculture is likely to
change. The predictions indicated moderate
increases in overall agricultural suitability to
2050, but there were significant regional
impacts for some crops. The study indicated
that varietal and/or crop substitution could
be a key strategy to adapt agriculture. For a
given site, there is high likelihood that crops
which are currently adapted to the condi-
tions will become maladapted, so that new
within-crop diversity will be needed to adapt
to future conditions, and under extreme
conditions different and well-adapted crops
will be required.
The list of studies on climate change impacts
is lengthy, and this section has only presented
a snapshot of studies for the three different
approaches. The overriding message from all
the studies is that considerable uncertainty
still exists in quantifying likely impacts of
climate change on crop productivity, as a
range of different methodological approaches
are used, with often conflicting results.
Further research is needed in synthesizing
results, as well as addressing model differ-
ences and taking more holistic approaches
to evaluating impacts.
Impacts on pest and disease prevalence
Global climatic change is also likely to impact
agriculture through shifts in patterns of
pests and diseases (organisms that range
from weeds, certain herbivorous insects,
arthropods and nematodes to fungi, bacteria
and viruses). Rising temperatures and varia-
tions in precipitation, humidity and other
abiotic factors are affecting the diversity and
responsiveness of agricultural pests and
diseases across diverse geographic ranges
(Rosenzweig and Liverman, 1992; Estay et
al., 2009). Of all the factors that influence
the productivity of agricultural pests and
diseases, temperature is cited as the most
important to insect ecology, epidemiology
and distribution, while humidity and rainfall
patterns and temperature are what define
the responsiveness of plant pathogens
(Coakley et al., 1999 cited in Hatfield et al.,
2008).
There are, however, few studies which
quantify likely impacts on pest and disease
prevalence due to the scarcity of system-
level studies that examine multi-trophic
complexities between causal and ancillary
agents (Newton et al., 2008). For example,
where crops are enriched by augmented
atmospheric CO2 concentrations, pest/
disease attacks are expected to negate opti-
mization effects. Moreover, where positive
impacts are highlighted (e.g. expanded range
of cultivars, climatic fertilization enhance-
ment), overriding negative consequences (in
terms of biodiversity, yield, mitigation costs,
etc.) are predicted to offset gains (Fuhrer,
2003 cited by Diffenbaugh et al., 2008; AEA
Energy & Environment and Universidad de
Politécnica de Madrid, 2007). While predic-
tions are more certain on which specific
pathogens and pests will thrive under greater
variability in climate, what is difficult to say
with certainty is what effects they will have
on similarly climate-stressed crops (Gregory
et al., 2009; Thomson et al., 2009). Thus, a
shroud of doubt still lingers as to the fore-
casting of climate warming on agriculture–
plague interactions. This is because, aside
from climate change effects, developing new
pest species and the spread of existing ones
are caused by (Cannon and Moran, 2008):
• natural expansion into unfilled ranges;
• active dissemination on vehicles;
• passive transport on traded plants and
plant products; and
• active flight (migrant species).
While this is true, Cannon (1998) deftly
describes the current state of affairs, saying:
Climatic phenomena, ecosystem processes and
human activities are interactive and
interdependent, making long-term predictions
extremely tenuous. Nevertheless, it appears
prudent to prepare for the possibility of
increases in the diversity and abundance of
pest species in the context of climate change.
26 A. Jarvis et al.
To that effect, and to the dismay of
economists­ and farmers alike, numerous
citations note the abundance and frequency
of pests and diseases as likely to increase as
local climates are adjusted outside their
previously bounded norms (Cannon, 1998;
Stireman III et al., 2005; FAO, 2008; Gregory
et al., 2009), especially in situations where
crops are moved to previously unsuitable
areas (Thomson et al., 2009). FAO (2008)
cites Cannon (2008) who in a cursory report
lists no less than 17 agricultural pests whose
geographic coverage, species incidence and/
or intensity will threaten to bring about
impacts on agricultural production under
climate change.
In a comprehensive report for the
European Commission Directorate-General
for Agri­culture and Rural Development
(2009), 16 different expert opinions are
aggregated and prioritized to declare the
‘medium’ confidence level of likelihood that
climate change effects in Europe are telltale
signs of increased risk of pests, diseases and
weeds (AEA Energy & Environment and
Universidad de Politécnica de Madrid, 2007,
Annex D). Tellingly, the same report lists the
increased risk of agricultural pests, diseases
and weeds in six of Europe’s eight agroeco-
systems as ‘high’ (the remaining two are
listed at ‘medium’).
Rising temperatures and
herbivorous pests
Under climate change, characterized by
increased temperatures and CO2 levels, the
fitness of plant herbivore pests is adjusting
as their distributions and niches vary along
with ambient conditions. In turn, their rela-
tionships with their natural enemies,
phenologies (i.e. arrival and emergence
times) and pressures from different pests
and pathogens are noted in the scientific
literature (Garrett et al., 2006; Ibáñez et al.,
2006). The physiological changes in plants
growing under new extremes and farmers’
adjusted management strategies will largely
determine how these dynamics play out (i.e.
it is difficult to say with certainty which
groups of contaminants will increase or
decrease and on which crops).
Numerous studies are finding that herbiv-
orous insect outbreaks are expected to
increase in both frequency and intensity as
global climate varies. Using the results of
inferential modelling, one study indicated
that the increased distribution and
abundance­ of Melanoplus sanguinipes, the
migratory grasshopper, was linked to corres­
ponding increases in temperature and mois-
ture over stretches of grain-producing areas
of Canada (Olfert and Weiss, 2006). The
increases in area susceptible to this native
insect pest under scenarios of temperature
increases of +2, +4 and +6°C were 17.3, 28.2
and 42.2%, respectively, signifying a great
loss in agricultural potential. Even among
tropical species changes are being measured
(Chen et al., 2009). The incidence of the
coffee leafminer (Perileucoptera coffeella) and
the nematode Meloidogyne incognita are
likely to increase in future in Brazil’s produc-
tion area. The number of coffee leafminer
cycles could increase by 4, 32 and 61% in
2020, 2050 and 2080, respectively, under
SRES A2 scenarios (Ghini et al., 2008). This
is more evidence to suggest that the range of
many pest herbivores may expand as a result
of decreases in cold stress.
Indeed, the likelihood is that the limita-
tions of many pest species to winter temper-
atures is being reduced (Newton et al., 2008).
Diffenbaugh et al. (2008) determined the
increased possibility of winter survival and
greater degree-day accumulations for four
insect pests in maize agroecosystems,
including the corn earworm, a migratory
predator of cotton, tomato and grains. They
indicate that a relaxation in cold limitation
would enable extension of the range of the
pest taxa, while the increase in heat accumu-
lation experience under warming regimes
has the potential to alter pest management
strategies across North America, harmfully
impacting seed and pesticide inventory
costs, yields and future effects in crop yield
variability. Similarly, as warmer winters are
realized the abundance of flea beetles
(Chaetocnema pulicaria) (the vectors for
Stewart’s wilt (Erwinia stewartii) bacteria)
will be likely to form a great threat to maize
crops (Harrington et al., 2001, cited in
Hatfield et al., 2008).
 Scenarios of Climate Change Within Agriculture 27
While the impacts of pests on yields and
productivity are undoubtedly affected by a
multitude of factors that are both biotic and
abiotic, effective and proven biological
controls in the form of pests’ natural preda­
tors are not to be overlooked as a factor that
impacts agricultural potential. Thomson et
al. (2009) address climate change effects on
herbivores and parasitoids of crops and
cultivars and how disruptions in climate
factors are adjusting fitness and competi­
tion for their natural enemies. Direct and
indirect aspects of phenological modifica­
tions in plants are affecting the fecundity
and abundance of herbivores, disadvanta­
ging their natural predators. Increases in
ambient CO2 and temperature, and adjust­
ments of humidity and precipitation rates
are adjusting the availability of food
resources for many pests, to their advantage
and disadvantage, depending on the species
involved. For example, both the larvae of
the gypsy moth, Lymantria dispar, and the
winter moth, Operophtera brumata, experi­
ence trouble with the change in food availa­
bility resulting from phenological changes
to their food sources (Thomson et al., 2009),
only there is evidence that the former can
actually take advantage of elevated CO2
when choosing to deposit its eggs on oaks
(Lindroth et al., 1993 cited in Cannon,
1998). There are also examples to the
contrary. Cannon (2008, in Annex 1 of FAO,
2008) notes how the cotton bollworm,
Helicoverpa armigera, scourge of the tropics,
subtropics and southern Europe, has been
increasingly seen moving inland since the
late 1960s. In situations where bollworm
dietary consumption of N is lacking (from
an indirect effect of higher CO2 levels), the
size of larvae was diminished, facilitating
predators’ chances (Coll and Hughes, 2008
cited in Thomson et al., 2009). Evidence
from a study of caterpillar–parasitoid inter­
actions across geographically dispersed
ecosystems (Stireman III et al., 2005)
suggests that there are limitations in the
way specialized parasites will be able to
track and regulate insect herbivore popula­
tions. This dynamic will be to the detriment
of agricultural land with huge cumulative
impact.
The benefits to the development of
natural pests and parasitoids of herbivores
are many despite the low certainty of techni­
cal feasibility for success (AEA Energy &
Environment and Universidad de Politécnica
de Madrid, 2007). Among other things, they
include a reduced risk of water contamina­
tion from pesticides (in systems that are
projected to see less or more variable precipi­
tation) and the fact that there are proven
cases of enemies apt to transfer zones along
with their prey (Thomson et al., 2009).
Nevertheless, climate change effects on
pests are complex and careful attention must
be applied to manage the effectiveness of
herbivore predators’ role in moderating crop
losses, especially as both cultivation and
species’ ranges (generally) expand (Thomson
et al., 2009).
Pathogens, virus vectors and diseases
As in the case of herbivorous pests, the
reaction of agricultural diseases to climate
change is specific to each strain and host in
diverse geographical areas, but likewise
poses itself as a real and intensifying threat.
In explaining the variability of future
impacts, FAO (2008) cites Chakraborty et
al. (2000), saying ‘Climate change could
have positive, negative or no impact on
individual plant diseases’ due to the lack of
comprehensive assessment (Gregory et al.,
2009). Despite this, evidence suggests that
wetter conditions will result in declining
yields from disease problems while warmer
conditions will enable the dispersal of
disease-bearing insects and the increased
survival of viruses (AEA Energy &
Environment and Universidad de Politécnica
de Madrid, 2007). The incidence of disease
propagation also depends on the level of
new agricultural intensification where the
means for new pathogens to travel by way
of irrigation canals, preferential flow and
runoff will be enhanced. Furthermore, the
significance of pathways for pathogens
depends on the underlying geographical
and geological properties (e.g. hydropho­
bicity, solubility, volatility) (Boxall et al.,
2009).
28 A. Jarvis et al.
In reference to biotic changes, climate
alterations may affect microclimates around
plants resulting in increased risk of infec-
tion from wetness and root diameter
(Garrett et al., 2006). Moreover, elevated
levels of CO2 can bring about positive effects
both indirectly (reduced expression of
induced resistance in plants) (Pangga et al.,
2004 cited in Gregory et al., 2009) and
directly (pathogen growth and fecundity)
(Chakraborty and Datta, 2003). The types of
provisions needed to combat disease and
viral risks to crops are complex. This is
because rusts and viruses transmitted
through insect vectors seem to be on the
rise, while pathogens such as Rhynchosporium
secalis that travel through water are less
likely to be seen in the heat of summer under
drier conditions. Wetter, less severe winters
are not precluded from many regional equa-
tions, making general conclusions hard to
come by (Newton et al., 2008).
Climate modifications affecting diseases
are also linked to food safety concerns. For
example the propensity for the spread of
foodborne pathogens from the greater
temporal range of diseases during planting
seasons has been noted (Ingram, 2008 cited
in Gregory et al., 2009). Crop contamination
from fungi similarly remains a threat. A
report by the UK Department for
Environment, Food and Rural Affairs (Defra)
(2008) highlights the trend towards larger
concentrations of microorganisms produ-
cing mycotoxins or aeroallergenic spores
under higher temperature regimes. As in the
cases of pests described above, a dual-edge
sword would exist with increases in tempera-
ture and humidity resulting in the propaga-
tion of more fungal diseases on the one
hand, while on the other some pests may
benefit from a shift towards their optimum
conditions, such as the case of the spruce
budworm (Choristoneura fumiferana)
(Fleming and Korpilahti, 1996 cited in
Cannon, 1998), and away from those of their
viral and parasitoid enemies. According to
Fernandes et al. (2004), the risk of Fusarium
head blight in wheat crops is very likely to
increase under climate change in southern
Brazil and in Uruguay.
Further demonstrating the complexity of
both plague and pest ecology are virus
vectors such as whiteflies (Homoptera:
Aleyrodidae) and the European large rasp-
berry aphid, Amphorophora idaei. Bemisia
tabaci is the most prolific of the whiteflies,
carrying some 110 plant viruses, of which
90% belong to a genus that severely damages
the plant physiology of its host (Morales,
2004). The European large raspberry aphid
is a vector of four viruses: raspberry leaf
spot virus, raspberry mottle virus, black
raspberry necrosis virus and Rubus yellow
net virus, that take as little as 2 min to be
transmitted upon contact (McMenemy et
al., 2009). Both pests will continue to enact
large economic losses as climate change
intensifies, especially given the diversifica-
tion of suitable planting regions.
Unfortunately, the expected increase and
overuse of pesticides (Aydinalp and Cresser,
2008; Hatfield et al., 2008; Antle, 2009;
Boxall et al., 2009; Thomson et al., 2009) to
address the greater risk of agricultural pests
poses detrimental effects to ecosystems.
Pesticide use is already cited as being greater
in warmer climates in the USA (Antle, 2009).
Additionally treacherous is the prospect that
increases in temperatures catalyse and
augment the volatility and toxicity of pesti-
cides jeopardizing regional atmospheric
conditions, reducing their capacity on pests
(Noyes et al., 2009) and further necessitat-
ing their overuse.
CO2-fertilization effects
One important prospect of global change in
climate that has received ample attention is
the sharp rise in the CO2 concentration and
its effects on plant growth and functioning.
The increased CO2 concentration in the
atmosphere is believed to provide enhanced
fertilization to plant growth, especially for C3
crops (Derner et al., 2003). The IPCC FAR
(2007) concluded that in isolation of climate
change, an atmospheric concentration of
550  ppm CO2 would result in productivity
increases of 10–20%, with increases of 0–10%
for C4 crops. When the combined effects of
enhanced CO2 are taken into account with
temperature increases, the productivity gains
are likely to be cancelled out. There continues
to be great uncertainty associated with
 Scenarios of Climate Change Within Agriculture 29
estimates­ of CO2 fertilization thanks to a
number of experimental complications which
we will briefly address later in this section.
Recent literature continues to question the
true level of fertilization, suggesting it to be
lower than originally thought (e.g. Woodward,
2002; Long et al., 2006).
Even pre-dating the global change
concerns, the effects of atmospheric CO2
enrichment have been studied for more than
a century in greenhouses, open-top chamber
and other enclosures to confine the CO2 gas
around the experimental plants (Kimball et
al., 2002). In these experiments the scien-
tific basis of physiological responses on the
level of plant individuals to elevated CO2
could be well established. A reduced stomatal
conductance under elevated CO2 conditions
leads to reduced water loss through transpir-
ation. This in turn is reported to increase
water-use and light-use efficiency. Through
the CO2-concentration effects on the growth
regulation protein ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco), a higher
rate of photosynthesis can be observed
(Drake et al., 1997). This stimulation of
photosynthesis is greater in plants that fix N
and have additional carbohydrate sinks in
their nodules which can be found in many
food crops and forages such as beans, peas,
groundnuts or white clover (Ainsworth and
Long, 2005).
The prospective changes in production of
the major grain and legume arable crops are
predicted to show great spatial variance with
anticipated production gains in the temper-
ate and boreal regions and production losses
in large parts of the tropics. While these
diametric changes occur, the global food
supply is expected to remain almost constant.
This optimistic view comes from the belief
that an elevated CO2 concentration will offset
the production losses anticipated because of
higher temperatures and changed precipi-
tation regimes. Evidence for this large
response to elevated CO2 is largely based on
studies made within small chambers at small
scales, which would be considered unaccept-
able for standard agronomic trials of new
cultivars or agrochemicals. Nevertheless esti-
mates of the ability of the globe to feed itself
are almost entirely dependent on data gained
in such facilities (Long et al., 2005).
Literally thousands of experimental stud-
ies have evaluated the response of crops to
the increases in atmospheric CO2 concentra-
tions expected to occur this century
(reviewed in Kimball et al., 2002) but most
information has been derived from experi-
mental studies that used greenhouses, arti-
ficially illuminated controlled environmental
chambers, transparent field enclosures or
open-top chambers. There have been large
concerns that these enclosures do not realis-
tically reflect the conditions in future open
fields since they suffer from a number of
experimental constraints and disregard
important effects such as the influence of
open-field winds on CO2 dispersal.
Furthermore the effects of elevated CO2
have been studied with non-limiting supply
of water and nutrients, and temperatures
have been kept near the optimum for crop
growth (Fuhrer, 2003). Large-scale free-air
CO2 enrichment (FACE) experiments allow
the exposure of plants to elevated CO2
concentrations under close to natural and
fully open-air conditions. Table 2.2 shows
the major FACE experiments that have been
conducted around the globe. These experi-
ments have focused largely on temperate
ecosystems, while tropical, boreal and arctic
systems have been largely ignored. Any seri-
ous commitment to discovering the response
of the terrestrial biosphere to atmospheric
change will critically require inclusion of
these key biomes (Ainsworth and Long,
2005).
The results of FACE do not strictly contra-
dict earlier findings from the greenhouse
experiments but put the optimistic expect-
ations of CO2 fertilization and its effect on
crop productivity somewhat into perspec-
tive. According to the review by Kimball et
al. (2002), elevated CO2 stimulates biomass
in C3 grasses by an average of 12%, grain
yield in wheat (Triticum aestivum L.) and rice
(Oryza sativa L.) by 10–15%, and tuber yield
in potato (Solanum tuberosum L.) by 28%.
FACE studies conducted since the mid-1990s
show an average crop yield stimulation of
only 17%, while previous estimates of CO2
effects on crop yield ranged from 28 to 35%
(Amthor, 2001; Jablonski et al., 2002). To
date, only two large-scale replicated FACE
facilities have reported elevated CO2
30 A. Jarvis et al.
Table 2.2.  Overview of large-scale free-air CO2 enrichment (FACE) facilities on food crops (Ainsworth
and Long, 2005).
Elevated CO2 Reference in
concentratrion which site is
Site Location (ppm)
Maricopa FACE Maricopa, Arizona, 550
USA
Rapolano Mid Chianti region, Italy 560–600
FACE
Rice FACE Shizukuishi town, Ambient + 200 Okada et al.
Japan
Soy FACE Champaign, Illinois, 550
USA
concentration­ effects on yields of C3 food
crops (wheat and rice). Several plant-level
feedbacks are known to prevent additional
investment in reproduction, such that yield
fails to reflect fully the increase in whole
plant carbon uptake.
The discrepancies between the results of
open-top chambers and other enclosures
and the FACE experiments have wide
importance as the chamber values have
formed the basis for projecting global and
regional food supply, and the stimulation
attributed to elevated CO2 concentration
has commonly been presumed to offset yield
losses that would otherwise result from
increased stresses, including higher tempera-
ture, elevated ground-level ozone and
changes in soil moisture (Ainsworth and
Long, 2005).
Even though the FACE experiments
already more-or-less realistically reflect field
conditions and enable us to estimate climate
change’s effect on agricultural production
more accurately, they nevertheless suffer
from a number of shortcomings. For one,
there is the concern that most elevated CO2
experiments only run for 5 years or fewer,
and thus may not capture longer-term
effects, especially acclimation phenomena
or downregulation to the higher CO2 levels.
Measurements have shown that with
prolonged exposure to elevated atmospheric
CO2, the photosynthetic rate gradually
declined, approaching or becoming even less
than the rate under ambient conditions
(Tang and Liren, 1998).
Steffen and Canadell (2005) argue that the
confidence in the reliability of the knowledge
First year of
described Ecosystem exposure
Lewin et al. Agronomic C3 1989
(1994) and C4 crops
Miglietta et al. Vitis vinifera 1995
(1997)
Oryza sativa 1998
(2001)
Leakey et al. Glycine max, 2000
(2006) Zea mays
base on the effects of elevated CO2 is rather
low. Difficulties arise when models, which are
usually based on empirical relationships, are
to be used for policy development. The effects
of elevated CO2 cannot be disentangled from
the effects of climate change on agricultural
production systems. Thus, when the cumula-
tive and interactive impacts of elevated CO2
and climate change are considered, our confi-
dence in the reliability of the knowledge base
for policy development has to be low. More
extensive FACE experimentation with the
major crops and within the major growing
zones will allow better forecasting of the
future food supply, given that predictions
currently based on chamber experiments
appear very optimistic.
Conclusions
The latest climate science paints a picture of
increasing temperatures (likely to be in the
range of 2–4°C to 2100), and a complex
change in rainfall regimes across the globe,
with some regions experiencing drying and
others significant increases. There is far less
certainty about changes in rainfall patterns
compared with the relatively high certainty of
temperature increases. The jury is still out on
the likely impacts of climate change on hurri-
cane events, but there is more certainty of
increases in extreme climate events such as
droughts, floods, hot days and high intensity
rainfall events.
The impacts of these changes on crop
productivity are likely to be negative. While
 Scenarios of Climate Change Within Agriculture 31
moderate increases in temperature may
bring about moderate increases in product-
ivity, beyond 1°C of warming the literature
tends to agree that impacts will be negative.
However, possible CO2 fertilization effects
may cancel out these losses, although signif-
icant debate exists as to the extent of CO2
fertilization to expect. The high degree of
uncertainty in climate projects for many
land areas makes the modelling of impacts
on agriculture difficult and produces contra-
dicting results. Research should be focused
on assessing impacts for those areas in which
a relatively high degree of certainty is present
in projections. Regional forecasts are needed.
A new generation of both GCMs and RCMs
is required in order to improve precipitation
forecasts and other Earth processes that
may influence agricultural production. In
the meantime, however, impact assessments
should focus on mid-term forecasts in order
to reduce the propagative errors in future
climate projections. In terms of enhancing
our understanding of the likely CO2 fertil­
ization effects, large-scale and long-term
FACE experiments with a focus on tropical
and boreal ecosystems are needed. A study
of multiple, interacting factors on produc-
tion systems would help to develop response
surfaces of the impacted system to identify
thresholds and/or tipping points. Systematic
pest and disease mapping and monitoring
will support a greater knowledge base for
evaluating the impacts of climate change on
pest and disease dynamics.
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 3
Economic Impacts of Climate
Change on Agriculture to 2030

David Lobell and Marshall Burke

Abstract
The global food economy is vast and technologically advanced, but none the less prone to substantial
negative outcomes in poor weather years. The economic gains or losses associated with climate change
will depend on the pace of climate change, the response of cropping systems – including the vast
number of growers, researchers, extension agents and others who determine how croplands are
managed – to these changes, and the response of global markets to resulting changes in crop yields.
We outline here the processes involved in each of these steps, and provide some estimates of likely and
possible extreme outcomes by 2030. Though adaptation holds great promise for reducing negative
outcomes, it is by no means guaranteed, and its realization will be likely to require significant advances
in crop research as well as in the ability of farmers to recognize climate trends and adopt appropriate
technologies.

Introduction of the crops themselves, but also on the

The consequences of climate change for the
modern food economy will depend on three
main factors. First is the nature of climate
change itself. For example: how fast will
temperatures rise, and where and by how
much will rainfall patterns change? In large
measure these changes will depend on emis-
sions of greenhouse gases (GHGs) and the
response of the climate system to these
gases, although changes in aerosols and land
use can also affect local climate trends,
particularly in agricultural regions (e.g.
Auffhammer et al., 2006; Lobell et al.,
2008a). Our understanding of future climate
rests largely on projections of climate from
general circulation models, as described by
Jarvis et al. (Chapter 2, this volume), which
embody a remarkably sophisticated but
inevitably limited description of the Earth’s
climate system.
The second key factor is the response of
cropping systems to changes in climate and
atmospheric constituents such as carbon
dioxide (CO2) and ozone (O3). This response
rests in large part on the biological aspects
physical environment (e.g. soil properties)
and crop and soil management. In particu-
lar, farmers may adjust management prac-
tices or crop selection to adapt to a new
climate, and advances in research or invest-
ments in rural infrastructure may greatly
enhance the number and effectiveness of
technologies available to them.
The third factor will be the response of the
food economy to changes in cropping systems
throughout the world. For instance, produc-
tion will shift to some degree away from farms
and regions most harmed by climate change,
and this may reduce the negative impacts on
overall food production and prices. Yet the
response of the global food economy to
climate cannot be viewed separately from
other major trends, as these will determine
the ability and willingness of people to buy
and sell food. For example, will regions hit
hardest by climate change have the resources
to import enough food, and will exporters
have policies in place to facilitate trade even
in years with especially poor harvests?
This chapter discusses the second and
third issues mentioned above (the first topic

38 © CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds)
 Economic Impacts on Agriculture to 2030 39
is addressed by Jarvis et al. in Chapter 2, this
volume.) The main objective is to provide a
context for the rest of the book by describ-
ing what is at stake (i.e. the expected impacts
in the absence of effective adaptations) and
what some of the key constraints to adapta-
tion are. Though the focus of the chapter is
on economic measures of impact, namely
total food production and food prices, we
emphasize that these can miss much of the
humanitarian costs of climate change. For
more discussion of potential impacts on
poverty and food security, see Lobell and
Burke (2009).
In the following section, we outline some
of the major non-climatic trends in the food
economy. In the section ‘Projecting Impacts
of Climate Change on Cropping Systems’ we
summarize some of the main processes by
which climate change will affect cropping
systems over the next few decades, includ-
ing the potential role of adaptation. As the
remainder of this book details specific adap-
tations, such as development of new crops
and management-based options like conser-
vation agriculture, we focus instead on
general issues and constraints to farmer
adaptation and trade responses. Finally, we
outline medium, optimistic and pessimistic
scenarios of economic impacts by 2030. We
focus on this time period because it repre-
sents a 20-year outlook that we consider to
be a typical time scale for developing new
crop varieties, which is the focus of this
book.
The Food Economy in 2030 Without
Climate Change
The modern food economy is much like
climate change itself: global in scope,
unprecedented­ in scale and constantly
changing. The scale of modern agriculture is
remarkable. Current production of cereals
amounts to over 2 billion t of grain/year,
roughly 15% of which is traded internation-
ally. There are roughly 1.4 billion head of
cattle, 1.0 billion pigs (over half of which are
in China) and 1.1 billion sheep in global agri-
culture, and a staggering 17 billion chickens
(FAO, 2005). The added value of agricultural
activity has been estimated as roughly
US$1.3 trillion/year out of roughly US$36
trillion in global economic activity. In devel-
oping countries, more than half of the over-
all work force is involved in agriculture (FAO,
2005).
Even without climate change, the food
economy in 2030 would look very different
from today for a few key reasons. First is the
expected growth in population, from roughly
6.7 billion people in 2008 to between 7.9
and 8.8 billion in 2030, with nearly all
growth occurring in the developing world
(United Nations Population Division
DoEaSA, 2009). The second reason is the
increased wealth among many of the histor-
ically poorer parts of the world, which is
universally associated with increased
consumption of animal products and reduced
intake of starchy staples (Pingali, 2007). As a
result of larger and wealthier populations,
total demand for cereal production is
expected to increase by roughly 50% between
2000 and 2030 (Bruinsma, 2003).
A third important demographic transi-
tion is the growth in urban relative to rural
populations, with urban populations in
developing countries expected to swell from
around 2.5 billion today (or ~40% of devel-
oping countries’ population) to around 4
billion in 2030 (~55% of the population)
(United Nations Population Division
DoEaSA, 2009). These relocations are
important for food systems because urban
dwellers tend to adopt more diverse diets,
shifting away from traditional cereals and
starchy staples into meat products, fruits
and vegetables, and easy-to-prepare wheat
products.
The fourth reason is that changes on the
supply side, such as improvements in the
physical and economic infrastructure in
many parts of the world, are making it easier
for agricultural goods to move within and
between countries. With agricultural
markets slowly liberalizing, and communi-
cation and transportation infrastructure
improving throughout much of the develop-
ing world, trade in food commodities is
expected to increase by 50% or more by 2030
(Bruinsma, 2003). As a result, any local
effects of climate change on food production
will be likely to be transmitted globally, with
global effects in turn felt locally.
40 D. Lobell and M. Burke
Finally, crop production technologies are
continually evolving and in some places
could even fundamentally alter the relation-
ship between weather and crop productivity.
For example, improved forecasts of growing
season rainfall and temperature could allow
farmers to adjust management to match the
expected weather conditions. Deployment
of existing technologies, such as irrigation,
will also continue to influence crop produc-
tion and its relationship with weather.
Projecting Impacts of Climate Change
on Cropping Systems
Attempting to disentangle the effects of
climate on cropping systems can be a daunt-
ing exercise. Agriculture involves so many
moving parts that it is nearly impossible to
perfectly understand the effects of any single
factor or set of factors. Yet the tremendous
importance of food production has motivated
thousands of studies on the topic, and as a
result there is a fairly good understanding of
some key processes. Since all of these studies
are in one way or another based on past
ex­perience from experiments or observa-
tions, it is often unclear how well they can
inform future scenarios where technologies
or climate conditions may be completely
different. For these reasons, any statement or
model projection about climate impacts has
associated with it ‘known unknowns’ (i.e. the
errors in our models that we are aware of)
and ‘unknown unknowns’ (i.e. the errors due
to factors not considered in our models). The
resulting uncertainties should therefore be
front and centre in any discussion of impacts.
Here we briefly outline what we do and do not
know about crop and farmer responses to
climate change, before providing a summary
of recent assessments of regional and global
scale impacts in the following section.
Crop responses
Temperature
Crop development and growth involves
several processes whose rates are affected by
changes in temperature. The net result of
warming on crop yields is positive in some
locations, namely regions where current
temperatures are cool relative to the crop’s
optimum, such as wheat in much of Canada
and China, maize in the northern extremes
of the USA, or rice in northern Japan. Yet
for most locations where major cereals are
grown, and nearly all locations within devel-
oping countries, warmer growing seasons
tend to result in less suitable conditions and
lower yields (Ramankutty et al., 2002; Lobell
and Field, 2007). Among the key reasons for
this are faster rates of crop development and
soil and canopy evapotranspiration (ET) as
warming occurs, with the latter resulting in
elevated water stress.
Though most cropping systems exhibit a
clearly negative yield response to warming,
the precise amount of yield loss per degree
warming is often not tightly constrained,
either from theory or observations. For
example, Fig. 3.1 displays estimates of rice
yield loss for different amounts of warming
in China and India, as estimated by several
crop modelling studies. Substantial differ-
ences between studies are evident, with as
much as a factor of two in some cases. Similar
levels of uncertainty are also often seen
when evaluating temperature responses
from statistical data. For example, in a study
that projected yield impacts in 2030 using
time series data and climate model projec-
tions for developing countries, the uncer-
tainty in temperature sensitivity was often
the single most important source of uncer-
tainty in projecting future impacts, surpass-
ing even uncertainties in future temperature
or precipitation change (Lobell and Burke,
2008).
Soil moisture
Soil moisture is also a critical factor deter-
mining crop yields. Variations in moisture
levels are mainly driven by precipitation, but
are also affected by temperature and other
factors that determine ET rates. In all but
the wettest environments, more rainfall
tends to raise yields. Some areas projected to
experience rainfall increases, such as eastern
Africa, could see yield increases with climate
change. However, the main areas where
 Economic Impacts on Agriculture to 2030 41

(a) China (b) India

20 20
Yield change (%)

Yield change (%)

0 0

−20 −20

−40 −40

0 1 2 3 4 5 6 0 1 2 3 4 5 6
Local temperature change (°C) Local temperature change (°C)

Fig. 3.1. Crop model estimates of rice yield changes for different levels of warming for (a) China and (b)
India, as reported in various studies. Black dots indicate effects without CO2 fertilization, and grey dots
with CO2 fertilization, with arrows connecting points from the same study. The only difference between
points connected by arrows is thus the simulated effect of CO2. Values were derived from three studies
for China (Matthews et al., 1995; Lin et al., 2005; Tao et al., 2008), and five for India (Matthews et al.,
1995; Lal et al., 1998; Saseendran et al., 2000; Aggarwal and Mall, 2002; Krishnan et al., 2007).

climate models agree that rainfall will
increase are high-latitude regions where
rainfall does not generally pose a severe limit
to crop growth. Many tropical and subtrop-
ical regions that experience frequent drought
stress are instead expected to see reduced
rainfall, such as southern Africa, much of
Mexico and south-west USA, southern
Europe and Australia. In most locations, the
direction of precipitation change over the
next few decades is ambiguous, with some
climate models showing more rainfall and
others projecting less. However, in many
places, even when rainfall is projected to
increase it is often by an amount that will be
insufficient to outweigh the negative effects
of warming. Hence, the effects of warming
still dominate both the projected yield
impacts and the associated uncertainties
(Lobell and Burke, 2008).
Carbon dioxide
A third critical factor affecting crop yield is
atmospheric CO2, which, like temperature,
is rising to unprecedented levels. Many
experiments with higher CO2 have been
performed in greenhouses or open-top
chambers in the field, showing a significant
enhancement of crop yields. This enhance-
ment is considered in most models, and
often results in net positive changes in yields
up to several degrees warming (see Fig. 3.1).
However, only a few studies have been
conducted under realistic field conditions
using free-air CO2 enrichment (FACE)
experiments. These latter studies have
tended to show lower yield responses than
the previous studies (Table 3.1), giving rise
to considerable debate on the expected
benefit of CO2 for yields.
Increased CO2 affects crops through two
mechanisms. First, it directly increases rates
of photosynthesis, in which CO2 is a critical
ingredient. Secondly, it leads to narrowing
of stomatal openings in leaves, which reduces
loss of water through transpiration. The
Table 3.1.  Mean estimates of yield increases (%)
for doubled CO2 from enclosure (chamber) and
FACE studies (adapted from Long et al., 2006).
Enclosure FACE
Crop studies studies
Rice  – 12
Wheat 31 13
Soybean 32 14
C4 crops (maize, sorghum)a 18  0
a Only a single FACE study has measured yield for a C
4
crop as of 2008 (maize in Illinois in 2004).
42 D. Lobell and M. Burke
photosynthesis effect appears to only matter
for C3 crops such as wheat and rice, because
intercellular CO2 levels in C4 crops like maize
are insensitive to ambient atmospheric
levels (Leakey et al., 2006). The transpiration
effect operates in both C3 and C4 crops, but
the magnitude of the response depends
greatly on soil moisture levels. It is therefore
difficult to extrapolate values from a small
number of experiments. Indeed, much of
the disparity between enclosure and FACE
results may be due to the fact that chambers
tend to limit root growth and raise canopy
temperatures, both of which can elevate
water stress relative to normal field condi-
tions (Leakey, 2009).
Nearly all FACE experiments have been
performed in temperate conditions, so less
is known about CO2 effects in tropical
regions. Maize responses in the FACE experi-
ments conducted in Illinois, for instance,
may be smaller than responses expected in
more drought-prone regions. More experi-
mentation and model validation in tropical
conditions is therefore an important need
for improving understanding of CO2
response.
Other factors
Most models used to assess future impacts
include some representation, albeit imper-
fect, of the effects of changes in average
temperature, precipitation and CO2 on
yields. Those that do not are at least explicit
about the absence of these commonly treated
factors. Yet many other processes are rarely
included in models but could potentially
have significant effects on yields in certain
situations. These include effects of pest and
disease responses to climate change, brief
exposures of crops to very high tempera-
tures (e.g. > 40°C), elevated ozone (O3)
(which is expected from higher temperatures
as well as greater pollution levels, especially
in China), more frequent flooding and poten-
tial loss of irrigation water because of
regional hydrological changes such as alpine
glacier melting. Though these are areas of
active research, quantitative understanding
of their potential roles is only beginning to
emerge. Therefore the assessment results
presented in ‘The Food Economy in a New
Climate’ section should be viewed in the
light of these unknowns.
One factor of particular concern to agri-
culture would be an increase in inter-annual
climate variability. In most regions there is
little agreement among climate models on
whether temperature variability will go up
or down or remain the same (Räisänen,
2002). In some areas summer temperature
variability is projected to increase because of
a reduction in soil moisture, which removes
an important dampener of temperature
volatility. However, it should be noted that
all climate models used in these assessments
do not include a representation of irrigation,
which should prevent large moisture changes
in many major food producing regions, so
that the climate effects of projected drying
may be overstated (Lobell et al., 2006).
Precipitation variability is projected to
increase in more locations and models than
temperature, but disagreement between
models is still quite large (Räisänen, 2002).
Some models suggest changes in import-
ant modes of variability, such as monsoons
and El Niño, so there appears at least the
potential for significant changes in vari-
ability (Meehl et al., 2007). At present,
however, there is wide disagreement among
models, and the ability of most models to
reproduce current modes of variability is
dubious. The fourth assessment report of
the Inter­governmental Panel on Climate
Change (IPCC) concluded, for example, that
‘there is no consistent indication at this time
of discernible future changes in ENSO [El
Niño-Southern Oscillation] amplitude or
frequency’ (Meehl et al., 2007). This is obvi-
ously an important area of active research,
but to date there is no compelling reason to
believe that increased variability and result-
ing effects on agriculture will approach the
effects of mean changes. For example
projected increases in temperature and
precipitation extremes, which are robust
across models (Tebaldi et al., 2006), are
driven much more by projected increases in
average temperatures than by changes in
inter-annual variability, even in models with
increased variability (Räisänen, 2002).
 Economic Impacts on Agriculture to 2030 43
Autonomous farmer and market
responses
One of the few universal truths in agricul-
ture is that farmers are constantly manipu-
lating the crop environment and, in most
places, changing their practices through
time. Therefore, in cases where climate shifts
represent a change that farmers perceive as
significant, they are sure to seek options to
adapt to the new conditions. It is therefore
imperative that any analysis of cropping
systems response looks beyond the biophys-
ical aspects of the soil–crop environment to
the human management dimension. Often
the distinction is made between those
changes that farmers will automatically
make without intervention, so-called
autonomous adaptation, and those that
require some form of intervention, the
so-called planned adaptations (e.g. educa-
tion, development of new technologies or
improved rural infrastructure).
For autonomous adaptation, the key issue
is not whether farmers will adapt, but exactly
what they might do and how effective they
will be. Similarly, food markets will always
adjust in response to productivity differences
between farms and countries, but the issue is
how effective these market responses will be.
Many adaptation options can be readily
observed by considering how farmers and
governments react to inter-annual weather
variations. These responses are typically a
mix of ex ante measures, which are taken in
advance of a climate realization, and ex post
responses, which are taken after the event is
realized. On the farm level, ex ante measures
can include options such as the diversifica-
tion of what, when and where crops are
planted in order to withstand the temporal
and spatial variability of rainfall in a given
area. For governments, they can involve
measures such as the development of early
warning systems to anticipate climate shocks,
or the expansion of social safety nets to deal
with these shocks’ inevitable consequences.
Ex post responses to an adverse climate shock
on the farm level can include drawing down
cash reserves or grain stores, borrowing
money, selling assets or finding work outside
agriculture. Governments might respond ex
post by distributing food aid or offering
short-term employment programmes for
those affected.
Many climate impacts studies either
explicitly or implicitly already take many of
these shorter-run adaptation options into
account. For instance, studies using process-
based crop models routinely allow planting
dates to shift in response to inter-annual
variation in the onset of the rainy season.
Similarly, studies that infer future climate
change impacts based on time series esti-
mates of historical crop response to climate
variation typically capture many of these
adaptations, because crop variables such as
yields are effectively measured net of any
adaptive action a farmer took in that year.
Quantifying the potential gains from
adaptation to longer-term shifts in mean
climate is more difficult, however. One
reason is that adaptation options available
in the short run might not be feasible in the
longer term. For example farmers’ ability to
draw down grain or cash reserves, or govern-
ments’ ability to deploy emergency aid,
might not be sustainable if every year is a
bad weather year. As a result, farmers might
adapt in ways distinct from these year-to-
year changes. These changes could include
growing varieties or crops they would not
grow in the current climate, or undertaking
more drastic shifts in their cropping calen-
dar, such as moving production to an entirely
different season in accord with the changing
climate. Some simulation studies find large
potential gains from such adaptations, for
instance with farmers in the temperate USA
able to offset most of their climate-change
associated losses by growing different
varieties and shifting their planting dates.
But employing these options will require
recognition that they are needed – that is
that farmers have correctly been able to
detect the signal of climate change in the
ongoing noise of climate variability. Evidence
is mixed on their ability to do so. For example
numerous studies in Africa have compared
farmer-perceived trends in climate with
actual observed trends, finding everything
from reasonable agreement between percep-
tions and trends to no agreement whatsoever
(Meze-Hausken, 2004; Maddison, 2007).
44 D. Lobell and M. Burke
Even when trends are clearly detectable,
however, the poorest farmers often demon-
strate little capacity to cope with sustained
adverse shifts in climate. The sustained
Sahelian drought of the 1970s and 1980s, for
instance, led to large-scale loss of life and
destruction of economic livelihood for farm-
ers and pastoralists in the region (Kandji et
al., 2006). Such anecdotes suggest the diffi-
culty poor farmers might have in adapting to
longer-run adverse climate shifts.
Planned adaptations
Where farmers are unable to autonomously
adapt, governments and other institutions
will have a role to play in making invest-
ments that help them adapt – so-called
‘planned adaptations’. The specifics of these
investments will depend on the nature of
the climate threat and the extent to which
farmers can respond on their own (thus the
urgent need for research on those topics).
Nevertheless, a few particular investments
seem to be sure bets. The first is increased
spending on the development of crop
varieties better suited to warmer climates.
The vast majority of poor farmers continue
to depend on improved germplasm of public-
sector origin, and with public-sector expend-
itures currently accounting for 94% of
agricultural research and development in
poor countries (Pardey and Beintema, 2002),
this dependence will be likely to continue.
Another area of promising investments
includes those that improve the function of
markets that serve the poor. For instance
input markets in many poor regions – nota-
bly Africa – are often poorly functioning and
hamper farmer response to changes in
climate. Government investment in roads
and ports could help reduce transport costs,
and recent foundation investments in agro-
dealer networks in eastern Africa have
shown promise in linking smallholders to
input markets (World Bank, 2008). Other
possible investments include expansion of
irrigation infrastructure, or further bolster-
ing of social safety nets.
What might these investments cost?
Historical public expenditures on crop breed-
ing have proven relatively cheap, especially
relative to their overall returns (Alston et al.,
2000). For instance, the Consultative Group
on International Agricultural Research
(CGIAR) achieved its pivotal role in sparking
and sustaining the Green Revolution on an
annual budget of US$10–50 million through-
out much of the 1960s and 1970s, and its
roughly US$400 million annual budget today
remains relatively small. Other planned
adaptations might be more costly – for
example one study indicates that doubling
the rate of irrigation expansion in Africa
would cost on the order of US$650 million
annually (Inocencio et al., 2007). A more
thorough review of agriculture development
costs and suggested priorities is given in two
recent reports, to which the reader is referred
for more information (World Bank, 2008;
The Chicago Initiative on Global Agricultural
Development, 2009).
The Food Economy in a New Climate
Given the processes of crop and farmer
response discussed above, what are the
expected effects of climate change over the
next 20 years? The answer is of course impos-
sible to know exactly, so instead we will
outline below what can be considered a
most-likely outcome, as well as plausible
worst-case and best-case scenarios.
Global scale yield changes
To begin, one can consider impacts of climate
change on average global yields of major
commodities. A recent study by Tebaldi and
Lobell (2008) attempted to estimate the
probability distribution function (pdf) of
impacts for maize, wheat and barley – three
crops for which the relationships between
average yields and crop-area weighted
temperature and precipitation are relatively
strong. The authors computed a pdf for
temperature and precipitation changes,
based on a Bayesian analysis of 18 climate
models. The median warming by 2030
(2020–2039 average) relative to 1990 (1980–
1999) was 1.6°C for maize, 1.4°C for wheat
 Economic Impacts on Agriculture to 2030 45
and 1.2°C for barley, with the slight differ-
ences due to the geographic distributions of
the crops. The estimated 5th percentile for
temperature, representing the level at which
there is only a 5% chance of warming by less
than this amount, was 0.9°C, 0.7°C and 0.5°C,
respectively, for the three crops (see Table
3.2). The warm end of the projections, or the
95th percentile, was 2.3°C, 2.0°C and 2.0°C.
Corresponding values for precipitation are
also shown in Table 3.2.
These climate changes were then used to
estimate yield impacts, using regression
models that related yields to average grow-
ing season temperature and precipitation.
The effects of elevated CO2 were also incorp-
orated using FACE experimental results. The
resulting yield impacts (Table 3.2) indicate
that, in a median scenario, wheat and barley
yields will be only moderately affected while
maize yields will be roughly 14% lower rela-
tive to no climate change. The ‘worst-case’
scenarios (5th percentile) were –24%, –2.4%
and –8.6%. Much of the disparity between
maize and the other crops is the smaller
beneficial effect of higher CO2, although
maize also appears to be slightly more
temperature sensitive to warming in its
current growing conditions (although maize
grows better in warm conditions than wheat
or barley, it starts from a much warmer base-
line.)
Importantly, this study considered only
average yields over a 20-year period, and not
Table 3.2.  Summary of probabilistic estimates of climate changes and yield impacts to 2030 relative to
1990 (data from Tebaldi and Lobell, 2008).
Maize
5th 95th
Median percentile percentile Median percentile percentile Median percentile percentile
Temperature 1.6 0.9   2.3   1.4
change (°C)
Precipitation –1.8 –8.5   4.2 –0.7
change (%)
Yield change –13.5 –23.0 –6.8 –5.4
(climate
effects only)
(%)
Yield change –14.0 –24.0 –7.2   1.6
(climate +
CO2 effects)
(%)
the occurrence of particularly bad years. The
latter could change by more or less than the
average, depending on whether and how
inter-annual variability changes (see the
‘Other factors’ section). Also, these impacts
consider only changes and effects of growing
season average conditions, and so would
miss any impacts of extreme events such as
floods or extreme dry spells. At the same
time, the impacts do not consider the poten-
tial effects of autonomous adaptation, which
would tend to improve yields. Thus, for
simplicity we can consider that these poten-
tial positive and negative biases would
roughly cancel each other and the estimates
of yield changes are a reasonable first-order
estimate.
Global scale economic impacts
Given these aggregate yield impacts, what
might the economic effects be? A simple esti-
mate would be to multiply the percentage
change in yield by the global production and
price of each crop, currently roughly 700
t/year and US$150/t in the case of maize.
Thus, a 14% drop in yields would correspond
to roughly US$15 billion/year at current
production and price levels, and even more
as global production grows. However, the
price effects of these production changes will
lead to adjustments in the economic system,
as farmers and regions with relatively lower
Wheat Barley
5th 95th 5th 95th
  0.7   2.0   1.2    0.5   2.0
–6.1   5.3 –0.5   –7.8   6.7
–9.4 –2.2 –8.8 –15.4 –3.0
–2.4   4.8 –1.9   –8.6   4.2
46 D. Lobell and M. Burke

impacts will produce more as their compara-
tive advantage improves. Percentage changes
in production will therefore be smaller than
average yield changes, while total economic
impacts could be smaller or larger depending
on price effects.
To fully sort out the eventual price and
economic effects requires a model of global
trade responses. For example Rosenzweig et
al. (1993) estimated regional changes in
grain crop yields, and then fed these into a
global trade model to simulate market
responses. The resulting global production
change was much smaller than the average
of regional yield changes, with the average
computed by weighting each region by its
production in the current climate (Table
3.3). Depending on the climate scenario,
which dictated both the overall impact and
the regional distribution, trade was able to
buffer production shortfalls to only roughly
one-quarter to one-half of the initial yield
change. Yet significant price increases
remained, ranging from 24 to 145% for the
three scenarios the authors considered, far
greater than the percentage drops in yields.
Returning to our estimates of yield
changes in 2030, if we consider maize repre-
sentative of the average C4 crop, wheat
representative of the average C3 crop, and C4
crops to comprise 40% of global grain
production, then the average cereal yield
changes by -5%, -11% and 0% in the
median, 5th percentile and 95th percentile
scenarios, respectively. This median scenario
is thus roughly close to the GISS scenario in
Table 3.3, so that we would expect a 24%
increase in price, assuming that the model
used in that study (the Basic Linked System
(BLS) world food model) provides a reason-
able representation of global trade. The 5th
percentile yield scenario would result in
roughly twice as much price increase, while
the 95th percentile would have no net
effect.
Interestingly, the Rosenzweig et al. (1993)
study reported a roughly constant propor-
tionality between price increase and
increased prevalence of hunger, with a 1%
increase in malnourishment for each 2.5%
increase in cereal prices. If we again trust
these numbers, then the median outcome
for 2030 would be an additional 10%
increase in malnourishment, with a ‘worst
case’ of roughly 20%.
There are, of course, important reasons
not to completely trust any of these numbers.
In particular, global trade models that rely
on equilibrium assumptions will miss
entirely the potential exacerbating effects of
policy responses or the influence of inves-
tors speculating in commodity markets.
Both of these were believed by many to play
an important role in the 2008 food price
increases. Moreover, many other assump-
tions in economic models are not adequately
tested. The above narrative is mainly
intended to provide some intuition on the
magnitude of possible effects and the
important mechanisms involved. Current
work is ongoing to understand in more detail
the propagation of yield changes throughout
the global economy, and the eventual impact
on regional and global commodity markets,
poverty and hunger.
Perhaps the most important and robust
message above is that only in a ‘best-case’
scenario do we estimate no net effect of

Table 3.3. Summary of impacts of doubled CO2 on average yields, production, prices and number of
malnourished (adapted from Rosenzweig et al., 1993; Rosenzweig and Parry, 1994).
Climate modela
GISS GFDL UKMO
Average change (%) in cereal yields, weighted by current production –5.3 –8.5 –18.5
Global change (%) in cereal production after economic adjustments –1.2 –2.8   –7.6
Price changes relative to baseline (%) 24 33 145
Increase in number of malnourished relative to baseline (%) 10 17   58
a GISS, Goddard Institute for Space Studies (4.2, 11); GFDL, Geophysical Fluid Dynamics Laboratory (4.0, 8); UKMO,

United Kingdom Meteorological Office (5.2, 15). Numbers in parentheses are global average change in temperature (°C)
and precipitation (%) for each model.
 Economic Impacts on Agriculture to 2030 47
climate change on average global cereal
yields by 2030. As pointed out by Tebaldi
and Lobell (2008), this conclusion is some-
what more pessimistic than the conclusions
of the IPCC, which states that temperate
regions will benefit from climate change up
to 3°C (Easterling et al., 2007). In part this is
simply a difference in emphasis on scales –
the IPCC states benefits for temperate
regions while noting that losses in tropical
regions will tend to negate these gains.
Equally, the disparity also probably arises
from the inclusion of adaptation in many of
the models used by the IPCC, although as we
note above these positive effects could be
cancelled by negative factors not considered
in most models. Other factors, such as opti-
mistic assumptions of CO2 fertilization in
some models, may also play a role.
In summary, climate change appears very
likely to cause downward pressure on aver-
age global yields by 2030. The economic
impacts of these yield changes are difficult
to estimate but could be considerable, with
as much as a 35% increase in prices. Although
these estimates do not include potential
gains from autonomous adaptation, they
also omit other potential negative factors
such as increased climate variability, pest
damage, and reactionary policy interven-
tions such as export bans in bad years.
Regional impacts
Although global scale economic impacts are
important, especially for consumers tied to
global markets, local and regional deviations
from global trends will also be of interest. In
particular, one may wish to know how
production will change in areas where the
ability to purchase food on global markets is
more limited, a situation that characterizes
many of the poorest areas in the world where
subsistence agriculture is common and local
prices respond directly to changes in local
production.
Uncertainties in crop yield projections
often increase as the scale of interest is
narrowed, in part because climate models
diverge more in their projections of tempera-
ture and rainfall at regional than global
scales. It is therefore difficult, for example,
to say whether impacts will be worse in one
country than another. None the less, some
general patterns emerge in most impact
assessments. First, crops grown today in
warmer (tropical) latitudes tend to fare
worse in a warmer world than crops grown
at higher latitudes. Thus projections for
countries such as Canada and Russia usually
indicate net positive impacts of climate
change and elevated CO2, while projections
for many developing countries are negative.
Secondly, those developing countries with
particularly hot growing seasons, particu-
larly sensitive crops, and/or particularly dire
rainfall projections tend to do worse. A recent
assessment of impacts by 2030 (Lobell et al.,
2008b) pinpointed southern Africa and
South Asia as two such regions, and argued
that substantial investments in adaptation
would be needed for these two regions to
avoid serious negative outcomes. In the case
of southern Africa, maize yields were
projected to fall by an average of 30% by
2030 from a combination of higher tempera-
tures and drier soils.
Conclusions
This chapter has focused on the global
economic impacts by 2030 that would occur
without effective planned adaptations, and
the constraints to achieving these adapta-
tions. Clearly, more work is needed to refine
our understanding of climate impacts on the
agricultural economy. Yet it is fairly evident
that, even in the next 20 years, climate
change has the potential to substantially add
to the dual challenges of feeding a growing
and wealthier global population and increas-
ing the rural incomes of the majority of the
world’s poor who continue to work in agri-
culture. Effective adaptation therefore repre-
sents a tremendous opportunity to improve
the future outlook for the world’s food econ-
omy. From a food security perspective, adap-
tation in southern Africa and South Asia,
and for the crops most important to those
regions, appears to be particularly needed
given the substantial climate risks faced in
these relatively food insecure regions.
48 D. Lobell and M. Burke
The question of which specific adaptation
approaches will be most effective is beyond
the scope of this chapter, but a topic much
deserving of future work. Many of the
opportunities for breeding and crop manage-
ment outlined in the next chapters will be
likely to play a crucial role in adjusting to a
changing climate (see the sections ‘Adapting
to Biotic and Abiotic Stresses through Crop
Breeding’ and ‘Sustainable and Resource-
conserving Technologies for Adaptation to
and Mitigation of Climate Change’ in
Chapter 1, this volume). But changes in
development of rural infrastructure and
institutions that can more effectively
manage risk and improve resiliency to
climate shocks are also likely to be import-
ant. One of the key challenges for research-
ers over the next decade will be to compare
these different strategies to each other, and
evaluate interactions between each strategy,
rather than considering each in isolation.
Such comparisons will be necessary to guide
investments and policies that result in
successful and cost-effective adaptation.
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 4
Preventing Potential Disease and
Pest Epidemics Under a Changing
Climate

Anne Legrève and Etienne Duveiller

Abstract
For a disease or pest to cause yield losses, the host and pathogen or pest must coincide within a
favourable environment. With changing weather patterns and cropping systems, abiotic and biotic
components influencing potential epidemics are modified and new interactions occur. Since they
affect plant phenology and the survival and multiplication rates of microorganisms and insects,
temperature and humidity are key factors of epidemics. The incidence of pathogens and pests has
noticeably evolved in recent years; globalization, in particular, has increased threats from new
transboundary pests and diseases. Factors driving new outbreaks include extraordinary climatic
events and trends in temperature selecting pathogens and their natural enemies towards new critical
thresholds for inoculum survival. Disease cycle components such as survival, infection, colonization
processes and latency period, in addition to production and dispersal of inoculum, are all affected.
Climate is most likely a strong driver of evolutionary change in plant and pathogen populations by
interfering with host–pathogen interactions, gene expression and population dynamics. Disease
monitoring and identifying the parameters affecting pest outbreaks improve epidemic risk assessment
and knowledge of the enemy. Strategies to prevent the negative effects of pests and diseases include
stringent quarantine regulations, adopting cropping systems that favour biocontrol or avoidance and,
most importantly, resistance breeding, cultural practices and sound phytosanitary measures. This
review highlights recent changes in microbial communities and the evolution of selected pathosystems
encompassing small grains, tubers and agroforestry. The value and effectiveness of integrated crop
management and sustainable approaches for controlling potential new disease and pest epidemics, in
the context of climate change, are emphasized.

Introduction atmospheric concentration of greenhouse

Preventing plant diseases has always been a
major concern in agriculture and a corner-
stone of breeding efforts to obtain higher
yields. Although recent decades have seen
major changes in ecosystems as a result of
agriculture intensification, producing
enough food for the growing population
remains a major global challenge. A range of
forces influence food systems and food secu-
rity, but the global food supply needs to
double by 2050, with the current world
population of about 6.7 billion being
projected to reach 9.5 billion by the mid-21st
century (Borlaug, 2009). Human-induced
climate change and increasing climate vari-
ability, resulting from the increase in the
50 © CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds)
gases (GHGs) (CO2, N2O, ozone), are recog-
nized unequivocally. The fourth report of
the Intergovernmental Panel on Climate
Change (IPCC) established by the World
Meteorological Organization (WMO) and
the United Nations Environment Programme
(UNEP) summarizes this evidence (IPPC,
2007). The most obvious effect is on the
global mean temperature, which is expected
to rise between 0.9 and 3.5°C by the year
2100. Cold days and nights and frost have
become less frequent over most land areas,
whereas hot days and nights are becoming
more frequent. The melting of the ice caps
and snow cover, resulting in rising sea levels,
the variation in the frequency, timing and
intensity of precipitation, leading to unusual
 Preventing Potential Disease and Pest Epidemics 51
floods mainly in coastal areas, and mid-term
or severe drought in other regions, are well
documented (IPCC, 2007; Chang and
Franczyk, 2008; Dukes et al., 2009). These
changes are not uniform (Motha, 2007). The
temperature increase is widespread across
the globe, but greater at higher northern
latitudes. Predictions indicate more droughts
in southern Africa, more wet periods in east-
ern Africa and no clear trends in western
Africa (Sanchez et al., 2009).
Since plant diseases reduce crop perform-
ance and are considerably affected by envir-
onmental parameters, it is likely that major
changes in ecoclimatic conditions will lead
to changes in plant disease frequency and
severity, threatening the quantity and qual-
ity of agricultural products (Mestre-Sanchis
and Feijoo-Bello, 2009). Several reviews
highlight the growing concern for the poten-
tial impact of climate change on plant
diseases (Manning and von Tiedemann,
1995; Coakley et al., 1999; Chakraborty et
al., 2000, 2008; Boland et al., 2004; Garrett
et al., 2006; Dukes et al., 2009; Gregory et al.,
2009). New cropping practices, globalization
and international trade have a rapid effect
on the plant disease spectrum. Recent
climatic changes undeniably observed world-
wide give a new dimension to the evolution
and distribution of plant pathogen popula-
tions resulting from crop intensification and
long-term climate evolution. This makes it
even more likely that plant disease evolution
and its control will require increased empha-
sis in the future under changing climate
scenarios. Although the epidemiology of
many plant pathosystems (Robinson, 1976)
is now better understood, it is difficult to
separate climate change effects on the
parameters affecting plant disease from
normal seasonal variations. The effects of
global climate change on plant diseases are
subtle, progressive and difficult to document
because of the scarcity of long-term data
sets (Jeger and Pautasso, 2008), resulting in
uncertainty about possible future scenarios.
Conclusions about a specific crop disease are
often deduced from limited studies on one
or a few specific physical variables (e.g.
temperature, CO2 concentration and
drought) conducted under controlled condi-
tions, whereas multiple interactions occur in
the context of climate change (Jahn et al.,
1996).
Studying and understanding the drivers
of change are essential if actions are to be
implemented that prevent or reduce their
impact. In this chapter we focus mainly on
factors affecting plant diseases and pests
from the perspective of agroecosystems and
food crops. Among these factors, increasing
temperature and variations in total relative
air humidity, total water availability and
rainfall patterns are likely to have a major
effect on plant diseases and pests. Before
discussing how these variables affect plant
pathosystems, we look at the concepts under-
lying plant disease and epidemics. The diver-
sity of the effects of climate change – driven
by evolutionary forces – on populations of
microorganisms, pests and plants, cropping
practices and yield are illustrated by recent
examples of food crop diseases and damage.
Strategies are outlined for mitigating emerg-
ing challenges resulting from new and poten-
tial epidemics affecting major crops.
Factors Leading to Potential Disease
and Pest Epidemics
Three essential components are required
simultaneously for a disease to occur: a viru-
lent pathogen, a susceptible host and a
favourable environment. A favourable envir-
onment includes all abiotic factors, such as
moisture (e.g. air humidity, rainfall and irri-
gation), temperature, sunlight, wind, nutri-
tion and soil quality, as well as biotic factors,
such as beneficial microorganisms and/or
predators that might interfere with the
pathogen or the plant. The relationship
between the three essential components of a
disease – pathogen, host and environment,
often referred to as the ‘disease triangle’ –
determines the outcome of that disease.
Pathogens and pests are very dependent on
environmental conditions for disease devel-
opment (Fig. 4.1). They often exist at low
levels, but erupt into epidemics under
favourable conditions.
Epidemics, as defined by Madden et al.
(2007), develop when changes in disease
52 A. Legrève and E. Duveiller

Evolutionary forces:
gene flow, genetic drift, selection,
mutation and recombination

Time

Pest/pathogen Host plant

population population
Virulence factors Phenology
Susceptibility

Environment
Meteorological conditions
(temperature, humidity, rainfall, wind, etc.)
Biotic factors
Alternative host plants, predators and pathogens
Antagonist/beneficial organisms
Human activities

Fig. 4.1.  The complex interactive epidemic tetrahedron illustrating the multiple interactions between the
three components of the ‘disease triangle’, the environment, the pest/pathogen and the host plant, and
the effect over time of the evolutionary forces on living populations leading to new diseases and pest
epidemics. The various components of the environment may interact differently on each step of the
infection cycle.

intensity occur in a host population over rhizosphere, including the introduction of

time and space. The two essential forces driv-
ing epidemics are the presence of host and
plant populations, and the dynamic processes
governing plant–pathogen interactions.
Disease infection cycles are characterized by
a series of steps, including inoculum survival,
infection, latency period, production of new
propagules and dispersal, leading to a second-
ary cycle or survival depending on the mono-
or polycyclic nature of epidemics. Each of
these steps is influenced by specific environ-
mental requirements which, in turn, could be
affected by climate change. Therefore, any
long-term or specific extraordinary atmos-
pheric event modifying the phyllosphere or
abiotic stress, would significantly modify the
interaction between the components of the
‘disease triangle’. With climate change, there
will probably be increases in some diseases
but decreases in others. The changes are
subtle, and they can be positive or negative
or even have a neutral impact on individual
pathosystems because of the specific nature
of the interaction of host and pathogen
(Coakley et al., 1999). A few examples here
illustrate the effect of these factors on disease
cycle components such as survival, the infec-
tion and colonization process, latency period,
and production and dispersal of inoculum
(Table 4.1).
 Preventing Potential Disease and Pest Epidemics 53
Survival
Changes in the environment can initially
affect the survival rate of pathogens and
pests. Higher minimum temperatures and
reduced frequency or intensity of cold days
favour the survival of pests with the falling
temperatures (Coakley et al., 1999). Leaf
rust epidemics caused by Puccinia triticina in
wheat in Kansas, USA were found to cause
higher yield losses over nearly two decades
in areas where the pathogen could over-
winter (Eversmeyer and Kramer, 2000).
Likewise, if the frost line moves north in the
northern hemisphere, higher average winter
temperatures could be associated with
higher survival rates of insect pests. Since
mild winters and warm springs contribute
to the survival and early development of
aphid vectors, they will favour barley yellow
dwarf (BYD) disease, one of the most severe
viral diseases in autumn-sown cereals in
Western Europe, transmitted by three aphid
species (Rhopalosiphum padi, Sitobion avenae
and Metopolophium dirhodum). However, hot
dry summers increase aphid mortality and
could halt the progress of the disease (Fabre
et al., 2005; Chancellor and Kubiriba, 2006).
Infection
The infection or penetration of a plant host
by infectious propagules is also determined
by specific environmental conditions. Fungal
pathogens usually require high relative
humidity or even free water for infection.
The infection process is limited by the
duration of surface wetness or high humidity
in most terrestrial environments (Magarey
et al., 2005). Various components of climate
change are likely to affect the level and
duration of humidity in the environment of
pathogens, including temperature and rain-
fall, and CO2 concentration through its effect
on plant growth and on the canopy micro-
climate. If a cropping system is subjected to a
dry environment, conditions become less
favourable for several foliar diseases, such as
powdery mildew of cereals caused by Blumeria
graminis, which requires high relative humid-
ity to penetrate host tissues and colonize the
leaf. Elevated concentrations of CO2 affect
infection of barley by B. graminis by increas-
ing mobilization of assimilates and limiting
the penetration of the pathogen (Hibberd et
al., 1996). Similarly, variation in the distribu-
tion and predominance of pathogens result-
ing in Fusarium head blight (FHB) of wheat
or scab, caused by several species of Fusarium
and Microdochium, is another example of how
climatic factors, particularly temperature
and moisture, determine the comparative
abundance of these fungi on infected wheat
ears. Scab is most severe in warm and wet
conditions at anthesis, and Fusarium gramin-
earum (teleomorph Gibberella zeae) is the
predominant species in these areas, although
FHB incidence has increased in cooler areas
(Xu et al., 2008), suggesting an evolution in
the factors influencing the disease cycle.
Whereas Fusarium poae is associated with
relatively drier and warmer conditions,
Fusarium avenaceum and Fusarium culmorum
are associated with areas where conditions
are cooler and humid. Thus, the environment
affects the infection and colonization
processes in different ways, which could lead
to shifts in the comparative abundance of
the species (Garrett et al., 2006). This could
eventually affect the spectrum of predomi-
nating mycotoxins generated by species caus-
ing FHB, which is a concern for food and feed
safety (Jennings et al., 2004). Similarly, crop-
ping practices such as zero and minimum till-
age could be associated with higher G. zeae
colonization in areas where wheat is grown
after maize, an alternate host for the fungus,
which highlights the role of survival capacity
in potential epidemics (Bateman et al., 2007).
In Europe, the occurrence of Phaeosphaeria
nodorum causing Septoria nodorum blotch in
wheat has become less important since the
late 1970s compared with the increased
prevalence of Mycosphaerella graminicola, the
causal agent of Septoria tritici blotch. Even if
changes in varieties and fungicide use partly
explain the higher prevalence of M. gramini-
cola over P. nodorum in recent years, the long-
term reduction in SO2 levels in the air is
correlated with the relative occurrence of
both fungi and explains a shift in their
respective incidence (Bearchell et al., 2005).
Recently, the deuteromycete Ramularia
 54
Table 4.1. Effect of climate and human-induced activities on disease cycle components in selected food crop pathosystems.
Disease cycle Crop Effect of climate and human-induced
component Pathogen/vectors Disease affected Observation activities References
Survival Fusarium graminearum, Fusarium head Wheat Fusarium head blight Maize grown at higher latitudes; over- Bateman et al.
Fusarium culmorum blight severity increase wintering of inoculum on previous (2007)
crop residues (maize) under zero
tillage
Puccinia triticina Leaf rust Wheat Yield losses increased in Over-wintering of inoculum Eversmeyer and
some areas Kramer (2000)
Rhopalosiphum padi, Aphid vectors of Oats, More BYDV Vector overwintering is favoured by mild Malmström and Field
Sitobion avenae, barley yellow barley, winters; CO2 increases root biomass (1997), Fabre et al.

A. Legrève and E. Duveiller

Metopolophium dwarf virus wheat and water-use efficiency of infected (2005), Chancellor
dirhodum (BYDV) plants (virus reservoirs) and Kubiriba (2006)

Infection Blumeria graminis Barley powdery Barley Reduced penetration of Dry air environment; elevated CO2 Hibberd et al. (1996),
mildew the fungus concentrations mobilize assimilates Jahn et al. (1996)
and plant response
Cochliobolus sativus Spot blotch Wheat More wheat areas Rising temperatures, particularly night Sharma and
affected and increased temperatures, increase host Duveiller (2004),
severity susceptibility Sharma et al.
(2007)
F. culmorum Fusarium head Wheat Incidence and severity Cool and humid environment favours Jennings et al.
blight disease (2004), Xu et al.
(2008)
F. graminearum Fusarium head Wheat Incidence and severity Warm and wet environment at anthesis Jennings et al.
blight favours disease (2004), Xu et al.
(2008)
Fusarium Dryland root rots Wheat Prevalence in dryland Drought-stress affected areas Duveiller et al. (2007)
pseudograminearum, and nematodes areas increasing; optimum irrigation less
F. culmorum, available
C. sativus and
nematodes
(Heterodera spp.,
Pratylenchus spp.)

Mycosphaerella Septoria tritici Wheat Prevalence and severity Reduction in SO2 in the air in last Jahn et al. (1996),
graminicola blotch increased in last decades; rainfall patterns Bearchell et al.
decades (2005)
Phaeosphaeria nodorum Septoria nodorum Wheat Prevalence decreased in Reduction in SO2 in the air in last Bearchell et al.
blotch Western Europe decades (2005)
Ramularia colo-cygni Ramularia leaf Barley Emerging disease Effect on host physiology influencing Schützendübel et al.
spot susceptibility to toxin (2008)

Latency Bemisia tabaci (whitefly) Vector of cassava Cassava Disease prevalence Reduction in generation time of the Chancellor and
mosaic virus associated with vector vector Kubiriba (2006)
multiplication

Preventing Potential Disease and Pest Epidemics

Vector of sweet Sweet Disease prevalence Reduction in generation time of the Chancellor and
potato chlorotic potato associated with vector vector Kubiriba (2006)
stunt virus multiplication
Cicadulina mbila and Vectors of maize Maize Disease prevalence Reduction in generation time of the Chancellor and
other leafhoppers streak virus associated with vector vector Kubiriba (2006)
multiplication
Phytophtora infestans Potato late blight Potato Model predicts fungicide 1–3°C temperature increase Kaukoranta (1996),
needed for longer accelerates pathogen multiplication; Boland et al.
period longer epidemics (2004)
Increased disease Warmer and wetter growing seasons Baker et al. (2005)
severity
Puccinia triticina Leaf rust Wheat Increasing incidence in Reduction in generation time FAO (2008)
new areas

Dispersal B. graminis Powdery mildew Barley, Spore dispersal favoured Dry air and warm temperature favouring Jahn et al. (1996),
wheat spore spread Chancellor and
Kubiriba (2006)
M. graminicola Septoria leaf Wheat Severity increased in rainy Rain splashes and rainfall patterns Jahn et al. (1996)
blotch years changed
P. infestans Potato leaf blight Wheat Severity increased in rainy Rainfall patterns changing Baker et al. (2005)
years
Puccinia graminis f. sp. Stem rust Wheat Ug99 dispersal Wind; outstanding storms Hodson et al. (2009)
tritici progressing to Iran

55
56 A. Legrève and E. Duveiller
colo-cygni, a pertotrophic fungus producing a
toxin that leads to leaf infection at a late
growth stage, has gained increasing import-
ance in Europe as the causal agent of a new
leaf spot disease in barley, Ramularia leaf
spot. The physiological status of the host
appears to govern the susceptibility of winter
barley to this pathogen (Schützendübel et al.,
2008). In southern Asia, spot blotch of wheat
caused by Cochliobolus sativus is more severe
under stress conditions, such as heat or poor
soil quality, and is therefore highly depend-
ent on plant physiology and growth stage
(Sharma and Duveiller, 2004). A 6-year study
at multiple sites has shown that disease
severity increased with rising temperatures,
particularly night temperatures, after anthe-
sis, suggesting that more wheat growing
areas will become affected by spot blotch,
along with heat stress affecting more regions
(Sharma et al., 2007; Ortiz et al., 2008).
Soilborne pathogens, including dryland
root rot and cereal nematodes, have a global
distribution and cause yield losses in rainfed
regions where cereals dominate the cropping
system and in irrigated areas where water
supply or rainfall might not always be
adequate, exposing the crops to water stress
and potential damage by these pathogens
(Duveiller et al., 2007). As climate change is
expected to increase the number of drought-
stress affected areas around the world, the
severity of root diseases such as common
root rot (C. sativus), foot rot induced by
several Fusarium pathogens, as well as nema-
tode problems, will increase when irrigation
becomes limited, as illustrated by the preva-
lence of these diseases in rainfed wheat-
based cropping systems in northern Africa
and western Asia.
Latency
Increasing temperatures reduce the latency
period or generation time, often measured
in degree days, and allow a higher number of
generations per season in terms of both
diseases and pests. This has a major effect on
polycyclic diseases and on diseases transmit-
ted by insect vectors. Generation time deter-
mines the amplification of plant diseases in
two ways: (i) it accelerates and increases the
inoculum load in a field or agroecosystem;
and, more importantly, (ii) it affects patho-
gen evolution rates and a pathogen’s capac-
ity to adapt to a changing environment often
faster than a host can respond. Leaf rust of
wheat will be favoured by higher tempera-
tures and might therefore spread to areas
where it is not currently important, such as
the facultative and winter wheat growing
areas of China, parts of Europe, the Pacific
north-west region of the USA and the winter
facultative wheat areas of Central Asia (FAO,
2008). In the case of potato late blight caused
by Phytophthora infestans, a model predict-
ing the date of outbreak in Finland based on
thermal time on rainy days suggests that
over a range of 1–3°C warming, the period
during which the disease needs to be control-
led by fungicide applications would be 10–20
days longer per 1°C (Kaukoranta, 1996). In
the upper Great Lakes region of the USA,
the risk of late blight of potato is increasing
because the climatological trends here have
resulted in warmer and wetter growing
season conditions (Baker et al., 2005). In
Africa, higher temperatures and rainfall
have led to an increase in the abundance of
whitefly, Bemisia tabaci, the vector of cassava
mosaic virus and sweet potato chlorotic
stunt virus, and of leafhoppers transmitting
maize streak disease (Chancellor and
Kubiriba, 2006).
Dispersal
The absence or scarcity of precipitation could
drastically limit the dispersal of splash-
dispersed propagules such as the Septoria
pycnidiospores produced by Mycosphaerella
graminicola in wheat or the sporanges and
spores of potato leaf blight. Rusts are well-
known examples of diseases dispersed by
wind over long distances. The recent outbreak
and dispersal of Ug99 (a highly virulent race
of Puccinia graminis f. sp. tritici that causes
susceptibility in most wheat cultivars) that
has moved from eastern Africa to Yemen
and Iran, now threatens southern Asia’s
wheat growing areas. Although the exact
cause of dispersal was not pinpointed, it is
 Preventing Potential Disease and Pest Epidemics 57
suspected that unusual wind and storm
events might have spread the inoculum to
Iran (Hodson et al., 2009).
Effects of Climate Change on
Evolutionary Forces,
Agroecosystems and Food Crops
Apart from the specific changes in disease-
infection cycle components, climate change
is almost certain to be a strong driver of
evolutionary change in plant and pathogen
populations by interfering with host–patho-
gen interactions, gene expression and popu-
lation dynamics (Harvell et al., 2002) (Table
4.2). Population genetic structure and
disease dynamics are very influenced by
pathogen–host–environment interactions
through the action of evolutionary forces.
McDonald and Linde (2002) identified five
forces affecting pathogen populations: (i)
mutation; (ii) genetic drift; (iii) gene flow;
(iv) asexual and sexual reproduction; and (v)
selection. Interspecific hybridization and
gene expression or functionality also influ-
ence the composition of pathogen popula-
tions. Climate change could influence
selection, an evolutionary force character-
ized by a directional process that leads to an
increase or decrease in the frequency of
genes or genotypes in a pathogen or pest
population. These forces affect biological
systems in various ways and influence
epidemiological dynamics and pathosys-
tems, depending on environmental condi-
tions. Through its impact on temperature or
humidity, climate change might select
stronger individuals. However, predicting
the potential responses of a pathosystem is
very complex because of the multivariate
nature of climate change and the multiple
effects of the biotic components of the
system, including the pathogen, its natural
hosts (crops or weeds) and its natural
enemies. Although most host–parasite
systems are predicted to experience more
frequent or severe disease occurrence with
warming, a subset of pathogens might
decline with warming, releasing hosts from
disease (Harvell et al., 2002). Some examples
of how climate change could influence evolu-
tionary forces, and the resulting conse-
quences are given hereafter (and see Table
4.3).
Mutation and genetic drift
Mutation is the ultimate source of genetic
variation, leading directly to changes in the
DNA sequence of individual genes and thus
creating new alleles in populations
(McDonald and Linde, 2002). The loss of
alleles over time, or genetic drift, can also
generate new diseases through the selection
of gene combinations that can adapt to a
new ecosystem. The evolutionary potential
of a small population is limited, but its adap-
tation capability to a new environment
should not be underestimated. Yellow rust is
a wheat disease known to occur in cool envir-
onments. It is caused by Puccinia striiformis,
a biotrophic asexually reproducing fungal
species harbouring new virulence strains
resulting from mutation. A study on P. strii-
formis diversity at global level has demon-
strated the recent intercontinental spread of
yellow rust (Hovmøller et al., 2008). New
epidemics in North America may be driven
by an increase in aggressiveness conferring
the ability to cause disease more quickly and
at temperatures once considered too warm
for the fungus (Milus et al., 2009). Particular
strains and their derivatives resulting from
mutation were found at multiple sites in
relatively warm or dry wheat growing areas
where severe yellow rust epidemics have
been observed in recent years. The genera-
tion time (latent period) was approximately
2 days shorter for ‘new strains’ compared
with isolates of representative strains
sampled before 2000 from multiple regions
in North America and Europe (Hovmøller et
al., 2008; Milus et al., 2009). The dramatic
increase in spore production potential
explains why a new and stronger strain can
spread rapidly at a global scale, for example,
by increasing the likelihood of ‘rare events’
occurring, such as long-range spore disper-
sal by wind or accidental spread (Wellings et
al., 1987; Brown and Hovmøller, 2002;
Hovmøller and Justesen, 2007; Hodson,
2009).
 58
Table 4.2. Effects of climate changes and human activities on evolutionary forces leading to a modification of pathogen populations resulting in new pest and
disease epidemics: examples from forestry, agroecosystems and food crops.
Affected Effects of climate changes and human
Evolutionary forces Pathogen Disease crop/species activities References
Mutation and Puccinia striiformis Yellow rust Wheat Intercontinental spread Hovmøller et al. (2008)
genetic drift Adaptation to higher temperatures; Milus et al. (2009)
reduction in generation time; increase in
spore production potential
Wind and accidental spread Wellings et al. (1987),
Brown and Hovmøller
(2002), Hovmøller and

A. Legrève and E. Duveiller

Justesen (2007), Hodson
­et al. (2009)

Gene flow Cryphonectria Asian chestnut tree American chestnut Introduction of pathogen into new Anagnostakis (1987)
parasitica blight ecological niches
Ophiostoma novo- Dutch elm disease Elm Introduction of pathogen into new Brasier (1991)
ulmi ecological niches
Puccinia graminis f. Stem and leaf rusts Oat Interactions at the agroecological Burdon and Thrall (2008)
sp. avenae, interfaces between wild host and
Puccinia coronata cultivated populations

Gene expression P. graminis f. sp. Stem rust Oat Temperature sensitive resistance genes Maertens et al. (1967)
or functionality avenae deactivated
P. striiformis Yellow rust Triticum turgidum As a result of gene Yr36 HTAPRa is Uauy et al. (2005)
ssp. dicoccoides effective
Xanthomonas Bacterial leaf blight Rice Xa7 resistance gene influenced by Garrett et al. (2006)
oryzae temperature
Blumeria graminis Powdery mildew Barley Mlo resistance gene disrupted by drought Newton and Young (1996)
stress
Magnaporthe Blast Rice Elevated atmospheric CO2 increases Kobayashi et al. (2006)
oryzae lesions possibly due to a reduction in
leaf silicon content

Barley yellow dwarf Barley yellow dwarf Oats, barley and Elevated atmospheric CO2 increases root Malmström and Field
virus (BYDV) (BYD) wheat biomass, photosynthesis and water-use (1997)
efficiency, favouring the persistence of
infected plants and virus reservoirs

Interspecific New Phytophthora Alder tree New aggressive species emerging naturally Brasier et al. (1999),
hybridization species from hybridization between Phytophthora Brasier (2001)
cambivora-like and Phytophthora
fragariae-like taxons
New Phytophthora Primula, New natural hybrids from Phytophthora Man in’t Veldt et al. (1998)

Preventing Potential Disease and Pest Epidemics

species Spathiphyllum cactorum and Phytophthora nicotianae
Pyrenophora tritici- Tan spot Wheat Horizontal transfer of ToxA gene from Friesen et al. (2006),
repentis Phaeosphaeria nodorum into the Stukenbrock and
P. tritici-repentis genome McDonald (2008)

Sexual and Phytophthora Late blight Potato Introduction of a second mating type to Goodwin et al. (1994),
asexual infestans new areas allowing sexual recombination McDonald and Linde
reproduction leading to more aggressive isolates with (2002)
high sporulation capacity and lower
generation time in the absence of host
resistance
a HTAPR, high temperature adult-plant resistance.

59
 60
Table 4.3. Synopsis of type of events and succession of effects resulting from the influence of climate change on evolutionary forces modifying host–pathogen
interactions and leading to new disease and pest epidemics.
Evolutionary forces Type of change occurring Induced effect Impact on host and pathogen Outcome
Mutation and genetic drift Ultimate change at DNA Adaptation to new Reduction in generation time, New epidemics resulting from
level environmental higher spore production dispersal or introduction to new
conditions areas including continents through
rare events and human activity
Gene flow Exchange between Increased population Variation in host resistance; New disease or pathogen emergence
populations of alleles or diversity variation in pathogen virulence;

A. Legrève and E. Duveiller

individuals new specific interactions
Interactions at the agroecological Introduction of pathogen into new
interfaces between wild host ecological niches
and cultivated populations
Gene expression or Phenotypic changes Change in pathosystems Host physiology and resistance Susceptibility or resistance to disease
functionality modified increased
Interspecific hybridization New species formed Change in pathosystems Shifts in the geographical Dispersal of exotic pests or pathogens
distribution of hosts and
pathogens
Horizontal gene transfer Emergence of new diseases
Sexual and asexual New aggressive strains Change in pathosystems Recombination leading to Emergence of new outbreak and
reproduction formed with high fitness emergence of more adapted chemical treatments; efficacy
aggressive isolates with high reduced due to rapid fungicide
sporulation and shorter resistance selection
generation time leading to
reduction of host resistance
capacity
 Preventing Potential Disease and Pest Epidemics 61
Gene flow
The gene or genotype flow, or the process
through which particular alleles or individu-
als are exchanged among separate popula-
tions (McDonald and Linde, 2002), is another
evolutionary force. While considered as a
unifying force that usually prevents popula-
tions from diverging by breaking down the
geographical or other boundaries that could
otherwise isolate populations, this evolution-
ary force could lead to the increased incidence
or severity of a disease or even to a new
disease. It tends to modify pathosystems
involving pathogens that produce propagules
with the natural potential of long-distance
dispersal, such as powdery mildew and rust
fungi, but also applies to pathogens with the
potential of short-distance spreading because
of dispersal by anthropogenic movement.
Depending on the distribution of populations
and the environmental conditions, which are
influenced by climate change, gene flow leads
to an increase in population diversity or to
the introduction of a new population in new
ecological niches, depending on the presence
or otherwise of another population of the
same species in the introduction area. The
evolutionary potential resulting from gene
flow allows for a variation in host resistance
and pathogen virulence, as well as new disease
or pathogen emergence.
In the newly colonized area, specific inter-
actions could lead to very diverse situations.
The introduction of the Asian chestnut tree
blight fungus, Cryphonectria parasitica, led
to the extermination of the American chest-
nut, Castanea dentata, from eastern USA
forests (Anagnostakis, 1987). Similarly, the
introduction of the aggressive pathogen
Ophiostoma novo-ulmi sp. nov. in North
America caused the extermination of many
elms that had survived the original epidemic
by Ophiostoma ulmi. Dutch elm disease
epidemics that resulted from the movement
of Ophiostoma species between and across
continents illustrate the dangers of moving
plant material around the world (Brasier,
1991). Climate change was not the cause of
the gene flow or its consequence in this case,
but these examples illustrate the high risks
of introducing pathogen genotypes into new
ecological niches where favourable inter-
actions allow the development of new
epidemics. The role played by wild oat popu-
lations in driving virulence evolution in the
pathogen populations of oat rusts (Puccinia
graminis f. sp. avenae and Puccinia coronata)
on oats in Australia also shows that inter-
actions at the agroecological interface
through gene flow between cultivated and
wild host plant populations could also alter
pathosystems (Burdon and Thrall, 2008).
Gene expression or functionality
Apart from the evolutionary forces influenc-
ing population diversity, climate change may
induce phenotypic change leading to differ-
ences in gene expression or functionality,
which also tend to modify pathosystems.
Increases in temperature can modify host
physiology and resistance by changing gene
expression and activity. For example, temper-
atures above 20°C deactivate temperature-
sensitive resistance to stem rust in oat
cultivars with Pg3 and Pg4 genes (Maertens et
al., 1967). In tetraploid wheat, lines carrying
Yr36, a previously unidentified stripe rust
resistance gene from Triticum turgidum ssp.
dicoccoides located on chromosome arm 6BS,
are susceptible to almost all stripe rust resist-
ance races of P. striiformis tested at the seed-
ling stage, but show adult-plant resistance to
the prevalent races in California at high diur-
nal temperatures (Uauy et al., 2005). This
high temperature adult-plant resistance
(HTAPR) is closely linked to the grain protein
content locus and has proven to be more
durable than seedling resistance due to its
non-race-specific nature (Uauy et al., 2005).
Temperature was also shown to influence the
resistance gene Xa7 in rice against bacterial
blight caused by Xanthomonas oryzae (Garrett
et al., 2006). Other environmental conditions
are also likely to alter the physiology and
functionality of resistance genes. In barley,
Newton and Young (1996) showed that the
mechanisms of Mlo-resistance, an important
powdery mildew resistance source, could be
disrupted following drought stress as cells
undergo expansion once water supply is
restored. The positive effect of the elevation
62 A. Legrève and E. Duveiller
of the CO2 concentration on plant growth is
now well recognized (Drake et al., 1997), but
the interference with pathogen development
will also influence the evolution of pathosys-
tems. Kobayashi et al. (2006) observed that
rice plants grown in an elevated atmospheric
CO2 concentration showed more leaf blast
(Magnaporthe oryzae) lesions than those in
ambient CO2. A relationship with leaf silicon
content, lower at high CO2 concentration,
and plant susceptibility was suggested.
Malmström and Field (1997) showed that
barley yellow dwarf (BYD) infection on Avena
sativa influenced plant response to CO2
enrichment by increasing root biomass
response, photosynthesis and water-use effi-
ciency. A change in the epidemiology of BYD
could occur at high CO2 content by increasing
the persistence of infected plants.
Interspecific hybridization
The most likely impact of climate change on
plant pathosystems would be shifts in the
geographical distribution of hosts and path-
ogens. Plant disease epidemics following the
dispersal of exotic pests or pathogens are
not rare (Brown and Hovmøller, 2002), but
the simultaneous occurrence of introduced
and resident species in a given ecosystem
could lead to the development of new patho-
gens. Interspecific hybridization between
Phytophthora cambivora-like species and an
unknown taxon similar to Phytophthora
fragariae has led to the emergence of a new
aggressive Phytophthora species pathogen
on alder trees in Europe (Brasier et al., 1999;
Brasier, 2001). Other natural hybrids of
Phytophthora nicotianae and Phytophthora
cactorum have demonstrated the evolution-
ary potential of this genus (Man in’t Veldt et
al., 1998).
Horizontal gene transfer due to nuclear or
somatic recombination is a further source of
new diseases and results from the simultane-
ous presence of different species in the same
environment. The species Pyrenophora tritici-
repentis, originally described as a saprophyte,
became pathogenic by inducing a damaging
disease of wheat called yellow spot or tan
spot. Friesen et al. (2006) suggest that this
change in virulence occurred after the trans-
fer of the ToxA gene coding for a protein-
aceous toxin from Phaeosphaeria nodorum,
the causative agent of blotch disease, into
the P. tritici-repentis genome. This example is
evidence of a new disease emerging because
of the interspecific transfer of a toxin gene
that changed a previously benign micro-
organism into an important pathogen
(Stukenbrock and McDonald, 2008).
Sexual and asexual reproduction
By affecting the distribution of gene diver-
sity among individuals in a population,
reproduction is a strong driver of evolution,
particularly for pathogens undergoing regu-
lar recombination, but also for asexually
reproducing pathogens because environ-
mental conditions promote the selection of
adapted individuals. Phytophthora infestans,
the causal agent of potato late blight, has
often caused major damage as the fungus
has moved into new countries. The Irish
famine, from 1844 to 1849, is a well-known
example illustrating how the introduction of
a new pathogen can affect food security in
the absence of host resistance. Until the late
20th century, with the exception of Mexico,
little genetic variation was found within and
among pathogen populations dominated by
a single mating. In the 1980s, the migration
of a the second mating type from northern
Mexico allowed sexual recombination in
P. infestans populations and the appearance
of increased aggressive isolates with a high
sporulation rate capacity and lower genera-
tion time (Goodwin et al., 1994; McDonald
and Linde, 2002). As new strains of
P. infestans evolve, new outbreaks of the
disease occur, which affects not only host
resistance capacity but also chemical treat-
ment efficacy as fungicide-resistant strains
are selected more rapidly (Anderson et al.,
2004).
Strategies for Mitigating the Climate-
related Effects of Pests and Diseases
on Crop Yields
Overall, strategies to limit the effect of
climate change on pests and diseases follow
 Preventing Potential Disease and Pest Epidemics 63
sound crop husbandry principles and do not
fundamentally differ from existing inte-
grated crop management practices, the basis
for sustainable agriculture (Oerke and
Dehne, 2004). More specific interventions
relate to limiting the movement of trans-
boundary pathogens and pests, evolving
germplasm improvement priorities in given
geographical areas, optimizing control prac-
tices and encouraging modelling and fore-
casting systems. When the enemies and
drivers of changes to host–pathogen inter-
actions are known, preventing potential
epidemics requires working against evolu-
tionary forces and minimizing inoculum
sources while remaining environment
friendly. In this context, breeding for host
resistance will continue to have a pivotal role
among the different options.
Limiting transboundary diseases and
controlling quarantine pests
Transboundary diseases and pests refer to
organisms that can be dispersed over a long
distance beyond the national or geograph-
ical boundaries (e.g. mountains and deserts),
such as rusts or migratory pests (e.g. locusts).
Transboundary plant pests are also quaran-
tine organisms that are absent from one
region or reported under control in one
country and could cause a threat if intro-
duced. With the globalization of trade and
international travel, quarantine measures
and early intervention are essential to
protect agroecosystems from the introduc-
tion of exotic pests and diseases and to
prevent the establishment and spread of
new epidemics­. This implies the develop-
ment and implementation of adequate poli-
cies, and the effective inspection and
certification of seed and plant materials free
from pathogens and pests (FAO, 2008).
Precautionary measures are also necessary
for endemic diseases characterized by the
existence of physiological races. Winds
disperse airborne pathogens such as soybean
and cereal rusts over a long distance. Soybean
rust caused by the Phakopsora pachyrhizi
fungus has been invasive in South America
since 2001 and was confirmed in the USA in
2004 (Oerke, 2006; Kumudini et al., 2008).
Recent examples­ show that wheat rust
epidemics have emerged from the introduc-
tion of a new virulent race following global
travel (Brown and Hovmøller, 2002;
Hovmøller et al., 2008), highlighting the
importance of public awareness of the need
to avoid introducing pathogens or pests. In
wheat, the rapid response of the scientific
community and the support given to wheat
research in reaction to the dispersal of Ug99,
the aggressive race of stem rust caused by P.
graminis f. sp. tritici, also illustrated how
internationally coordinated breeding efforts,
backstopped by advanced research insti-
tutes, can mitigate the threat caused by the
migration of a race that is virulent against
90% of commercial wheat cultivars world-
wide (Singh et al., 2008). The same principle
applies to preventing the introduction of the
vectors of viral diseases. The monitoring of
emerging diseases and early diagnostic
capacity to identify new problems in the
field are therefore essential. Wheat blast, an
emerging disease caused by Magnaporthe
grisea (Duveiller et al., 2007), presently
restricted to warmer growing areas in the
Southern Cone, deserves attention in
preventing the pathogen, or its wheat-
affecting pathotype, migrating or being
introduced into climatically­ comparable
wheat systems in other regions.
Improving plant resistance to biotic
stresses
Breeding for disease and pest resistance is
one of the primary objectives of breeding
programmes. It requires an understanding
of parasite biology and ecology, disease
cycles and drivers influencing the evolution
of plant–pathogen interactions because,
unlike other traits, pest resistance is influ-
enced by genetic variability in the pest popu-
lation, especially in diseases. With evolving
pathogen populations and changes in fitness
favouring new pathotypes, as a result of
climate change or not, the continuous
improvement of resistance to biotic stresses
is paramount in maintaining yield potential
and genetic gains. Resistance is essential for
food security in economies where farmers
cannot afford to use chemical control, and
64 A. Legrève and E. Duveiller
increasingly in advanced countries where
the reduction in authorized active ingredi-
ents on the market, due to environmental
concerns of the public and policy makers,
has meant that farmers have to rely more on
host resistance. There are numerous exam-
ples documenting the progress in host resist-
ance in many crops. Sayre et al. (1998)
demonstrated the impact of breeding for
leaf rust resistance over time using a set of
Mexican wheat cultivars released between
1966 and 1988. Data showed that while yield
potential (yield with fungicide applied) had
increased significantly (0.52%/year), pro­gress
protecting the yield potential due to incorp-
oration of leaf rust resistance genes (yield
without fungicide) was higher (2.1%/year).
Progress in biotechnology, particularly
marker assisted selection, will contribute to
making breeding for resistance against diffi-
cult traits more efficient. Tactics and meth-
ods might change, depending on the
pathosystems, but breeding for durable
resistance is perhaps the major objective of
plant breeders. Although durable resistance
can be confirmed only after a cultivar has
been grown on a large scale for a relatively
long time, it is generally accepted that it is
more likely to be achieved by breeding for
non-race-specific resistance and the accu-
mulation of minor genes conferring partial
resistance. There has been a major genetics
and breeding emphasis in recent decades on
slow-rusting, minor-resistance genes with
additive effects against leaf and yellow rust
pathogens in wheat. The use of Sr2 and Lr34
and minor genes in controlling stem rust
and leaf rust in wheat illustrates this
approach (Singh et al., 2000). A study with
Lr34 isolines showed yield losses of approxi-
mately 15% associated with leaf rust infec-
tion in the presence of the genes, while when
Lr34 was absent losses were 40–85%,
depending on planting date (Singh and
Huerta-Espino, 1997). Gene pyramiding and
the deployment of major genes could offer
an option for a rapid response against a new
threat. However, these remain controversial
because although the selection of new
complex races is possible, the effect might
not last in the case of a rapid race evolution.
The development of resistant material
against the Sr24 virulent variant of Ug99
confirms the value of breeding strategies
based on minor genes, as demonstrated by
the development of new genotypes (Singh et
al., 2009).
In the context of climate change, breed-
ing for resistance against several pathogens
should not be disconnected from improving
resistance to abiotic stresses, particularly for
water-use efficiency and heat tolerance,
because abiotic stress factors could enhance
the disease effect. Spot blotch of wheat is
more severe under heat stress, and therefore
improving yield potential and heat toler-
ance, particularly to night heat during grain
filling, should contribute to lower disease
losses (Sharma et al., 2007). It is also likely
that improving root systems and drought
tolerance could increase resistance to soil-
borne foot rot diseases. Breeding priorities
in a given geographical region might be
evolving as new crops and systems are intro-
duced. Stubble-borne diseases such as tan
spot (P. tritici-repentis), Fusarium ear rot or
Septoria leaf blotch in wheat receive more
attention in areas where reduced tillage is
being adopted.
Agricultural practices: rotation, time of
planting and avoidance
In many regions, intensification has replaced
diverse agroecosystems and increased the
vulnerability to pest attacks. Monoculture
and growing ‘megacultivars’ (varieties occu-
pying millions of hectares, such as the wheat
cultivars ‘PBW343’ and ‘Inqualab’ in India
and Pakistan) increase the likelihood of
pathogen recombination or mutation by
selection pressure. Changes in seasonal
weather patterns could also contribute to
the displacement of land use and crop-
producing areas (Kiritani, 2007). While
temperate cereal-based systems will expand
to higher latitudes, reduced water availabil-
ity in Africa could reduce the areas under
maize and force farmers to grow sorghum
instead, which will bring new requirements
for pest and disease control (Chancellor and
Kubiriba, 2006). The package of technolo-
gies available, including resistant cultivars,
 Preventing Potential Disease and Pest Epidemics 65
might not always be readily available when a
new crop is cultivated. Growing soybean in
the summer in Yaqui Valley in Sonora,
Mexico, has stopped because of the lack of
resistance against whitefly, Bemisia argenti-
folii (= B. tabaci B biotype). In Brazil, wheat
blast has been a major constraint to expand-
ing wheat cultivation in the Cerrados.
Traditional crop management approaches
such as rotation, intercropping, crop diversi-
fication and switching cultivars are import-
ant adaptive strategies for minimizing the
amount of inoculum. Earlier or later plant-
ing may help prevent the window of climatic
conditions (e.g. rainfall) favouring a patho-
gen outbreak or reduce the exposure to a
critical abiotic stress (e.g. heat) that predis-
poses a crop to diseases such as spot blotch
in wheat in southern Asia (Sharma and
Duveiller, 2004). The management of rice
tungro bacilliform virus transmitted by
Cicadellidae can be improved by the synchro-
nized planting of partially resistant geno-
types (Cabunagan et al., 2001). Conservation
agriculture practices are being adopted in
many areas, partly to reduce production
costs but more importantly to address envir-
onmental concerns such as soil degradation
and declining water resources. Reduced till-
age and residue retention will shift the
breeding emphasis towards resistance
against stubble-borne diseases such as tan
spot and Septoria diseases of wheat.
However, conservation agriculture has the
advantage of stimulating microorganisms
and arthropod diversity, bacterial antago-
nisms and biocontrol. Mazzola (Chapter 11,
this volume) illustrates the effects of
suppressive soils in controlling some soil-
borne diseases. With population growth and
global warming leading to soil degradation
and declining water resources, cereal systems
will evolve in various regions, such as south-
ern Asia, to cope with the increasing demand
for food. New agronomic practices such as
direct-seeded rice, alternate water supply
(dry/wet), reduced tillage or the use of
permanent raised beds will require monitor-
ing to observe the potential effect on pests
and diseases. The study of pest and disease
injury profiles (Savary et al., 2006) under
current and new agronomic practices will
determine future needs in breeding and crop
protection strategies.
Chemical control
Chemical control is among the options avail-
able for limiting yield losses (Oerke, 2006).
Intrinsic pest/pathogen characteristics (e.g.
diapause, life cycle, generation time, mini-
mum, maximum and optimum growth
temperatures, and host interaction) and
intrinsic ecosystem characteristics (e.g.
monoculture and biodiversity) lead to
changes in microorganism populations. An
increase in pest infestation might lead to
greater use of chemical pesticides to control
them. It has been estimated that the use of
fungicides for controlling late blight in
potato will increase by 15–20% in the coming
decades (Fry and Goodwin, 1997). Climate
change could change the efficacy of crop
protection because precipitation patterns
and increased CO2 may affect the residual
effect of active ingredients on the leaf or
their uptake in the case of systemic
compounds, respectively (Coakley et al.,
1999). Pesticide use could also have detri-
mental effects on beneficial organisms, as in
the case of the brown plant hopper
(Nilaparvata lugens) on rice (Savary et al.,
2006). The reduction in the number of
authorized active ingredients on the market
for ecological reasons could reduce chemical
control options and lead to a situation that
will require a better knowledge of the target
populations and their resistance levels, the
further development and application of
integrated pest management (IPM) tech-
niques, and the use of prediction systems in
precision agriculture.
Forecasting models
Modelling is a tool for developing early warn-
ing systems and reducing the application of
chemicals. Forecasting models need to be
valid and to predict actual field observations
adequately. With climate change, the chal-
lenge is to take account of the variability in
disease epidemiology. Disease forecasting
66 A. Legrève and E. Duveiller
systems using non-linear responses to
temperature and leaf wetness offer more
potential for representing these effects
(Bourgeois et al., 2004). However, although
modelling is becoming more sophisticated,
the main concern for these studies on the
impact of climate change on crop production
is to include the changed pest dynamics and
intensity (insects, plant pathogens and
weeds) that are generally ignored under
climate change (Scherm, 2004). Savary et al.
(2006) have reviewed the types of crop loss
knowledge and various models integrating
environment, disease and losses. The ulti-
mate objective is to contribute to decisions
on whether or not to apply a pesticide and
minimize economic losses. With the devel-
opment of new tools such as geographic
information systems (GIS) and remote sens-
ing, access through the Internet to site-
specific weather information without
sensors could offer new possibilities for fore-
casting conditions that favour a disease or
pest (Magarey et al., 2001). The Integrated
Pest Management – Pest Information
Platform for Extension and Education
(IpmPIPE) site illustrates the effectiveness
of Internet-based tools to monitor and
manage new disease outbreaks such as that
of soybean rust in the USA (USDA, 2009).
Research on the relationship between leaf
area and relative yield is expected to lead to
the development of a yield-loss prediction
model specific to the impact of soybean rust
(Kumudini et al., 2008; University of
Kentucky, 2009). The ‘Rustmapper’ system
is another example using the Internet that
allows the risk of dispersal of the wheat stem
rust pathogen by tracking unusual climatic
events (winds, rainfall) to be assessed
(Hodson et al., 2009). Similarly the Desert
Locust Information Service (DLIS) based at
the Food and Agriculture Organization of
the United Nations (FAO) headquarters in
Rome sends early alerts and forecasts for
each country on desert locust plagues; it
generates maps showing where solitary and
gregarious hoppers and adults are observed
(FAO, 2009). The locust forecasting system
is based on a network of surveillance, remote
sensing, meteorological information and
GIS analysis. The impact of climate change is
also under investigation.
Conclusions
Climate change, with its multiple effects on
ecosystems, is likely to change the inter-
actions between an infectious propagule, a
susceptible host and favourable environ-
mental conditions, leading to the develop-
ment of new epidemics. The effect of plant
diseases and insect pests on crop damage is
recognized because agriculture is highly
influenced by climatic factors. This review
highlights the difficulty of separating normal
seasonal variations from global climate
change effects, due either to subtle changes
in temperature or humidity or to extraordin-
ary events. The lack of long-term data is also
hampering the ability to document with
certainty changes in pest and disease
profiles. Crop intensification and economic
forces have a strong and direct impact on
pests and diseases because changing crop-
ping systems drive changes in pathogen and
pest populations in a relatively short time.
Climate change is expected to have major
effects on population thresholds of micro-
organisms and disease vectors. The dynam-
ics affecting host–pathogen interactions
lead to the selection of new pathotypes or
pathogens. They also determine the emer-
gence of new diseases and pests. Options to
prevent these effects have been discussed.
Among these strategies, breeding for pest
and disease resistance is critical and will
remain an essential part of germplasm
improvement. Increases in yield per unit of
area will continue to depend largely on more
efficient control of (biotic) stresses rather
than on an increase in yield potential
(Cassman, 1999). Integrated crop manage-
ment is therefore the basis for sustainable
agriculture. The range of options for adapt-
ing to the changes increases with technolog-
ical advances. It is anticipated that modelling,
remote sensing and spatial integration of
critical climatic information and its access in
near real time through the Internet will also
contribute to precision agriculture.
 Preventing Potential Disease and Pest Epidemics 67
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 5
Breeding for Adaptation to
Heat and Drought Stress

Matthew P. Reynolds, Dirk Hays and Scott Chapman

Abstract
Crops respond similarly to drought and heat stress: life cycle is accelerated reducing photosynthetic
capacity via restricted leaf area and duration. Metabolism is inhibited at temperature and water
potential ranges outside those optimal for growth. Reproductive processes are impaired when stress
occurs at critical developmental stages reducing seed set. Both stresses can be exacerbated by nutrient
deficiencies and biotic factors while elevated CO2 levels may partially ameliorate stress in C3 species.
Although stress adaptive traits – and consistent quantitative trait loci associated with them – are used
to design new cultivars, the physiological and genetic bases of adaptation are only partially understood.
Therefore, plant selection requires empirical approaches such as multi-location testing across
representative environments, while detailed characterization of target sites permits genotype ×
environment interaction to be dissected, providing feedback into breeding and research. Precision
phenotyping approaches assist by dissecting yield into its physiological components and have
application in breeding and gene discovery. Examples of stress-adaptive traits which have been
selected for in several species include deeper roots enabling plants to remain hydrated under drought
and permitting canopy cooling under heat stress, transpiration efficiency, delayed senescence in
sorghum, and synchronous flowering in maize. New traits and genes must be identified – perhaps
among crop wild relatives or in model species – that permit cultivars to be buffered against temporal
variation in water supply, adapt to higher temperatures without loss of water-use efficiency, and
tolerate sudden extreme climatic events or combinations of stress factors. Examples of past successes
and promising new approaches are discussed.

Introduction Among the major cereal crops, rice,

The Intergovernmental Panel on Climate
Change (IPCC) predicts that by 2050, mean
temperatures around the planet may rise by
between 2 and 5°C or more and atmospheric
CO2 concentration are likely to be > 550 ppm
(cf. 380 ppm at present). Tropical and semi-
tropical climates in particular are expected
to experience dramatic increases in temper-
atures, as well as more variable rainfall
(Jarvis et al., Chapter 2, this volume). Of
serious concern is the fact that most of the
world’s low-income families dependent on
agriculture live in vulnerable areas, namely
in Africa and Asia. Not surprisingly, climate
change has been acknowledged as a major
challenge to future food security (Lobell and
Burke, Chapter 3, this volume).
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 71
sorghum and maize are relatively well
adapted to high temperatures, given their
sites of origin and the fact that they have
been grown extensively in tropical regions
during the modern agricultural era. It can be
argued that extant breeding programmes
are already geared up to delivering germ-
plasm that will be productive in ‘warmer
than average’ years (Braun et al., Chapter 7,
this volume). For these cropping systems, a
substantial challenge associated with climate
change will be to stabilize their performance
in drier than average years. Ongoing efforts
to genetically improve maize (Bänziger et al.,
2006; Campos et al., 2006), rice (Wassmann
et al., 2009) and sorghum (e.g. Mason et al.,
2008) under water deficit will need to be
intensified to maintain and increase
72 M.P. Reynolds et al.
productivity­. Temperate cereals such as
wheat and barley, on the other hand, are
relatively well adapted to drier environ-
ments, being grown widely throughout the
world in semi-arid regions such as North
Africa, Central Asia and Australia. Ongoing
breeding work has made steady progress in
improving performance (e.g. Trethowan et
al., 2002; Ammar et al., 2008). However,
performance of cereals shows substantial
loss at high temperature (Wardlaw et al.,
1989; Reynolds et al., 1994) and significant
breeding effort will be required to maintain
their productivity under warmer conditions.
For C3 cereals (wheat, barley, rice), there is
some evidence that increased CO2 will
partially offset the effects of higher tempera-
ture and drought through improvements in
the water-use efficiency, however, the extent
of its impact on productivity is still in doubt
(Leakey et al., 2006).
Already, a large portion of global varia-
tion in crop yield is explained by rainfall and
temperature fluctuation and this will
increase as climate changes (Jarvis et al.,
Chapter 2, this volume). Specific scenarios
in which their detrimental effects are likely
to be most devastating include situations
where irrigation water is not available to
compensate for decreased rainfall or to miti-
gate the effects of higher temperature via
evaporative cooling of leaves, and in agro-
ecosystems where soils have been degraded
to a point where they no longer provide
sufficient buffer (e.g. adequate water-hold-
ing capacity) against drought and heat stress.
These problems cannot be addressed by
improving genetic adaptation to heat or
drought stress alone and readers are referred
to the chapter on conservation agriculture
(Hobbs and Govaerts, Chapter 10, this
volume); investment in genetic improve-
ment will be best realized if crops are grown
in well-managed soils that maximize expres-
sion of genetic potential, buffer the crop
against weather fluctuations, and guarantee
long-term returns by stabilizing the natural
resource base.
The remainder of this chapter will outline
the challenges of genetically improving
major food crops to adaptation to warmer
and drier conditions. We first consider that
research focused on genetic improvement
should be conducted with adequate know-
ledge of the environmental factors that
interact with trait expression to ensure that
genetic gains achieved in breeding environ-
ments are realized at target locations and
across years (Salekdeh et al., 2009). This
section is followed by an overview of the
genetic and physiological basis of adaptation
to drought and heat stress in the context of
traits having known or probable economic
significance. Several case studies of success-
ful genetic improvement strategies are
presented in a range of cereal crops. Lastly
there is a discussion on promising future
approaches to raise the genetic yield thresh-
old of crops under heat and drought stress,
and on strategies to accelerate genetic gain.
Characteristics of Heat and Drought-
stressed Environments
Drought
Productivity gains in water-limited environ-
ments involve many traits (Fig. 5.1a) that
tend to show a complex interaction with a
number of environmental factors. Patterns
of rainfall distribution across target regions
as well as between seasons are unpredictable
and their variance is expected to increase as
climate changes (Jarvis et al., Chapter 2, this
volume).
Drought-prone environments also exhibit
wide variation in other climatic characteris-
tics, biotic stresses and edaphic factors
including micronutrient deficiency (like
zinc) and mineral toxicity (such as boron,
salinity and sodicity). With a few exceptions,
combination effects have received scant
attention, despite the fact that crop product-
ivity is especially vulnerable when more than
one abiotic stress is experienced (Mittler,
2006). The main implication for breeding
will be a need to develop genetic combina-
tions of traits that are robust to inter- and
intra-seasonal variation in drought intensity
– as well as the other exacerbating factors
mentioned – while ensuring that such culti-
vars remain responsive to favourable years.
Because understanding of the physiological
 Breeding for Adaptation to Heat and Drought Stress 73

(a) YIELD = WU × WUE × HI (drought stress)

Photoprotection (WUE)
• Leaf • Pigments
morphology – chlorophyll a:b
– wax – carotenoids
– posture/rolling • Antioxidants
stay-green)

Partitioning (HI) Water uptake (WU)

• Floret fertility • Ground cover – protects soil
– flowering synchrony (maize) moisture
– panicle extrusion (rice) – early vigour
• Stem carbohydrate storage • Access to water by roots
and remobilization – cool canopy
• Grain harvest index – osmotic adjustment
– Rht alleles

(b) YIELD = LI × RUE × HI (heat stress)

Photoprotection (RUE) Efficient metabolism (RUE)
• Leaf • Pigments • Starch synthase
morphology – chlorophyll a:b • Dark respiration rate
– wax – carotenoids • CO2 fixation
– posture/rolling • Antioxidants – CO2 concentrating mechanism
– Rubisco activase
– Rubisco specificity

Partitioning (HI) Light interception (LI)

• Floret fertility • Rapid ground cover
• Stem carbohydrate storage • Stay-green
and remobilization
• Grain harvest index Water uptake (RUE)
– Rht alleles • Access to water by roots
– vascular system to match
evaporative demand

Fig. 5.1.  Conceptual models for traits associated with adaptation to: (a) moisture-stressed environments
grouped according to main drivers of yield under drought (yield = water uptake (WU) × water-use
efficiency (WUE) × harvest index (HI) as defined by Passioura, 1977); (b) hot-irrigated environments
grouped according to main drivers of yield without water limitation (yield = light interception (LI) ×
radiation-use efficiency (RUE) × harvest index (HI)). Spike photosynthsis may have higher WUE
associated with recycling of respiratory CO2. Other traits presented are discussed in the text (and
references therein); however, the list is not exhaustive, and while some of the traits have been
successfully combined to achieve cumulative gene action for drought adaptation in wheat (Reynolds et
al., 2009), traits cannot be assumed to be additive, or necessarily of equal value across a range of target
environments because trait × environment interaction can be expected.
74 M.P. Reynolds et al.
and genetic basis of adaptation to water-
limited environments is incomplete, breed-
ing progress will require empirical approaches
such as multi-location testing (Braun et al.,
Chapter 7, this volume).
However, detailed characterization of
target environments can help with the inter-
pretation of adaptive responses, as well as
germplasm deployment. Recent develop-
ments in the area of geographical informa-
tion systems (GIS) make it more feasible
than in the past to characterize target envir-
onments. For example, with GIS software,
weather data can be interpolated across
regions that may encompass relatively few
weather stations, while databases permit
additional information on soil properties
and cropping systems to be entered and read-
ily accessed (Hodson and White, Chapter 13,
this volume). Such a database can be further
enhanced by the calculation of stress indices
(via crop simulation models) and summaries
of weather variables coinciding with differ-
ent stages of growth. When combined with
phenotypic data from field trials, such indi-
ces and summaries of stress patterns can be
applied in advanced statistical analyses to
indicate the traits and genetic backgrounds
associated with adaptation to specific envir-
onmental factors (see Crossa et al., Chapter
14, this volume). Molecular information can
also be used to help explain genetic bases of
genotype × environment interactions (Boer
et al., 2007).
Heat
High temperature stress is relatively predict-
able in some regions (e.g. parts of South Asia
and sub-Saharan Africa) increasing slowly in
a way that permits plants to acclimate. In
other regions, however, stress can occur quite
suddenly and may be accompanied by desic-
cating winds (e.g. the Great Plains in the USA
or North Africa). An additional dimension to
heat stress is relative humidity (RH). In moist
tropical regions, high RH further ex­acerbates
heat stress in two ways. Saturated air:
(i) reduces the potential for evaporative cool-
ing of plant organs; and (ii) is accompanied
by higher night temperatures.
While optimum mean temperatures for
different crop species are reasonably well
defined, ranging from the mid-teens (degrees
Celsius, °C) for wheat, to the twenties for rice,
maize, sorghum and soybean (CCSP, 2009),
air temperature is not necessarily an indica-
tor of the stress experienced by plants.
Specifically in low RH environments, plant
temperature may be several degrees below
ambient air temperature, assuming sufficient
water is available to match evaporative
demand (Amani et al., 1996). Therefore, the
actual heat stress experienced by a plant will
be a function not only of air temperature but
also of agronomic and genetic factors deter-
mining the potential for evaporative cooling
(Table 5.1).
Interaction of heat and drought with
elevated CO2
By 2050 atmospheric CO2 levels are expected
to be around 550 ppm. In C3 species such as
wheat and rice, the elevated CO2 level is
expected to increase productivity due to the
improvement of CO2 diffusion through
stomata and a consequent effect on photo-
synthesis. However, a complex of interactions
can arise among plant development, growth
and environment variables. Plants that have
acclimated to high CO2 and grown new leaves
over time (with typically fewer and smaller
stomata) do not show the same high photo-
synthesis rates as a ‘normal CO2’ plant will
under short periods of exposure (Leakey et
al., 2009; Parry and Hawkesford, Chapter 8,
this volume). Consequently, the observed
increases in yield have been only in the order
of 10–20% for crops like wheat, when grown
in open-top chambers with elevated CO2.
Recent open-air experiments for maize have
demonstrated no increase in yield in field-
level experiments under well-watered condi-
tions and CO2 levels of 550 ppm, although
there was substantial reduction in water use
(Leakey et al., 2009). These types of findings
have implications for irrigation needs in C3
versus C4 crops under elevated CO2: that is, if
growth is stimulated in C3 crops, then more
water may be required to maintain additional
leaf area, and in dry areas, there may be an
Table 5.1.  Factors affecting plant canopy temperature (CT) in crops.

Estimated range
Factors Mechanism of effect (°C) Referencea
Environmental Ambient air temperature Equilibrium with air ~50
Radiation load Plant organs absorb energy directly ~10 Loomis and Connor (1992)
Rainfall Potential for evapotranspirative cooling ~10 Ehrler (1973)
Relative humidity Potential for evapotranspirative cooling ~10 Ehrler (1973)
Soil depth and water capacity Potential for evapotranspirative cooling ~10 Kirkegaard et al. (2007)

Breeding for Adaptation to Heat and Drought Stress

CO2 level High CO2 can interact with cooling capability via stomatal ~2 Leakey et al. (2009)
development and regulation
Agronomic Planting time Realized impact of ambient temperatures on development ~10 McMaster et al. (2005)
and growth patterns
Planting method (e.g. row Affects boundary layers and energy balance ~2 Loomis and Connor (1992)
spacing)
Irrigation Potential for evapotranspirative cooling ~10 Ehrler (1973)
Tillage system Affects water infiltration into soil ~10 Hobbs and Govaerts (Chapter
10, this volume)
Residue management Residues impact on water fluxes at soil surface ~10 Hobbs and Govaerts (Chapter
10, this volume)
Weed control Weeds compete for water ~5 Oerke (2006)
Pests and diseases Can affect stomatal behaviour ~2 Rosyara et al. (2008)
Genetic Ground cover and establishment Bare soil heats quickly affecting crown temperature ~20 Ross et al. (1985)
Canopy architecture Area and structure affects energy absorbed and water ~2 Araus et al. (1993)
demand to balance exchange of CO2
Stomatal conductance Determines rate of evaporative cooling ~2 Amani et al. (1996)
Root growth Area and pattern affects water supply ~5 Reynolds et al. (2007)
Root signalling Affects rate of evaporative cooling ~2 Davies et al. (2005)
Pigment composition Affects energy absorbed ~2 Tardy et al. (1998)
Epicuticular wax Affects energy absorbed ~2 Richards (2006)
Phenological pattern E.g. floral structures have lower evapotranspiration rate ~2 Ayeneh et al. (2002)
than leaves
a Refers to mechanism rather than actual temperature differences, which are estimated by authors.

75
76 M.P. Reynolds et al.
increased risk of drought impact through the
exhaustion of stored soil water compared
with ‘slower’ growing crops.
However, as temperatures increase CO2
solubility declines relative to O2. Thus, for C3
crops the compensation of elevated CO2 can
be confounded by photorespiration. Also,
elevated temperatures are known to impair
Rubisco activase, the enzyme responsible for
removing the inhibitory ribulose 1,5-bis-
phosphate from a deactivated Rubisco (Parry
and Hawkesford, Chapter 8, this volume). As
such, some of the apparent benefits of
elevated CO2 may be offset by higher
tempera­tures, causing photosynthesis to be
energetically more expensive.
Biotic stress
Although beyond the scope of this chapter,
changing patterns of drought and heat, as
well as elevated CO2, are likely to be accom-
panied by a change in the spectrum of biotic
stresses. For most cereals, more tropical
environments are also associated with
greater numbers of foliar pests and diseases;
therefore climate change would be likely to
result in increased risk of epidemics (Legrève
and Duveiller, Chapter 4, this volume). In
dry regions, root diseases such as nematode
infestation are also problematic since they
further reduce the plant’s ability to extract
scarce water (Nicol and Rivoal, 2007).
Physiological Basis of Stress
Adaptation in Major Crops
Physiological effects of water stress
Water deficit leads directly to stomatal
closure and reduces the potential for CO2
fixation relative to well-watered plants.
Closure is caused both by hydraulic effects
and by chemical signalling, the latter being
an adaptive function that increases transpir-
ation efficiency (Davies et al., 2005) and is
the basis of the common practice of deficit
irrigation in water-scarce environments
(Fereres and Soriano, 2007). A consequence
of reduced transpiration rate may be that
plant organs experience heat stress (see next
section). Increasing water deficit leads to
changes in tissue water potentials that may
be suboptimal for expansive growth and
metabolism (Hsiao, 2003). Osmotic adjust-
ment is commonly observed under water
deficit to resist further dehydration and to
maintain favourable gradients of water
potential that permit growth to continue
(Morgan, 2000). If these drought-adaptive
strategies are insufficient to maintain
growth and development, reproductive
behaviour will be impaired leading to floret
sterility and/or inadequate levels of assimi-
lation to sustain seed growth (see Barnabas
et al., 2008). Cessation of growth may be
followed by tissue dehydration if water stress
is not relieved, potentially resulting in
damage to the photosynthetic apparatus
and other metabolic processes (Ghannoum,
2009). A more recently observed phenom-
enon under drought is that of micronutrient
deficiency caused by reduced transpiration
rates under water deficit. Zinc is involved in
detoxification of reactive oxygen species
(ROS) so low rates of passive uptake coupled
with increased production of ROS under
moisture stress combine to exacerbate
drought-stress symptoms in soils that are
zinc deficient (Bagci et al., 2007).
Physiological effects of heat stress
A principal effect of heat is to accelerate
growth and development, shortening the
window of opportunity to intercept radia-
tion. As a result of accelerated growth rate,
total leaf area available for photosynthesis is
frequently reduced also, further reducing
yield potential. For example, wheat has been
shown to lose 3–4% of yield/°C above the
optimum daytime temperature of 15°C
(Wardlaw et al., 1989). However, the actual
degree of heat stress experienced by a crop
depends on the interaction of many environ-
mental and genetic effects (Table 5.1),
including evaporative cooling which may
vary considerably throughout the crop’s life
cycle and at a local level. When evaporative
cooling is insufficient to maintain plant
organs at close to optimal temperatures, the
 Breeding for Adaptation to Heat and Drought Stress 77
plants will experience metabolic inefficien-
cies associated with functioning outside
optimal temperature ranges (Burke et al.,
1988). For example, starch synthase may be
rate limiting to grain filling at warmer
temperatures (Hurkman et al., 2003) and
elevated temperatures also increase wasteful
photorespiration in C3 species (Parry and
Hawksworth, Chapter 8, this volume).
Increased rates of dark respiration are
another source of lost productivity at high
temperature and remain an important chal-
lenge to stabilizing crop productivity in the
advent of climate change; even a tropical
crop such as rice loses yield potential at
warmer night temperatures (Mohammed
and Tarpley, 2009). As under water deficit,
high temperature stress can also lead directly
to sterility by impairing meiosis, gametogen-
esis and fertilization (Barnabas et al., 2008;
Hedhly et al., 2009). In an agronomic
context, heat stress can lead to macronutri-
ent deficiency associated with the inability
of transport processes to match accelerated
growth rates (Rawson, 1986).
Short-term extreme increases in tempera-
ture of 5–10°C can have quite catastrophic
effects on yield especially if they occur at
critical stages of development. This sensitiv-
ity is not exclusive to cool season crops but is
also observed in relatively heat-adapted
crops, such as rice (Wassmann et al., 2009).
Adaptive strategies
There are a number of strategies to amelior-
ate the effects of drought and heat stress.
Agronomic strategies
Agronomic strategies include: (i) modifying
planting time such that critical growth
stages do not coincide with stressful condi-
tions (McMaster et al., 2005); (ii) resource
conserving technologies that help available
growth inputs, especially water, to be
supplied as optimally as possible to the crop
(Hobbs and Govaerts, Chapter 10, this
volume); and (iii) good husbandry to avoid
weeds, pests and diseases from further
exacerbating­stress.
Trait-based strategies
The most effective genetic strategy has been
to change the phenological pattern of the
crop so that critical growth stages do not
coincide with stressful conditions or simply
to finish the life cycle early before severe
stress conditions occur (Ludlow and
Muchow, 1990). Another is to minimize the
occurrence of stress through development
of a good root system, which in the case of
drought permits water to be accessed deeper
in the soil (Lopes and Reynolds, 2010) and
in the case of heat permits transpiration
rates that better match evaporative demand
(Amani et al., 1996), thereby permitting
maximal carbon fixation with the benefits of
canopy cooling. In environments where
‘extra’ water is not available to mitigate
stress, other stress-adaptive strategies
include a range of leaf canopy traits such as
epicuticular wax, pigment composition, leaf
angle and rolling, etc. that influence radia-
tion load and photosynthetic response,
while increased transpiration efficiency
permits available water to be used more
effectively (Richards, 2006). Maintaining
foliar and root health through genetic resist-
ance to pest and diseases is usually consid-
ered prerequisite. Such effects can be
cumulatively significant – and will interact
with other environmental and agronomic
effects such as irrigation and tillage systems
(Table 5.1). Examples of their application
are discussed subsequently in the context of
specific breeding efforts, as well as in various
books (see Ribaut, 2006; Jenks et al., 2007).
Cellular and molecular strategies
It is expected that the growing understand-
ing of the cellular and molecular basis of
adaption to heat and drought stress will
have significant impact in breeding for
climate change in future decades. For exam-
ple, it is established that plant response to
drought involves multiple mechanisms asso-
ciated with water relations, chemical signals
and membranes (Chaves et al., 2003). In
maize, part of the effect of drought on floret
abortion – a trait which has a disproportion-
ate effect on harvest index compared with
78 M.P. Reynolds et al.
its effect on water-use efficiency – has been
traced to several genes involved in sucrose
metabolism (Boyer and McLaughlin, 2007).
Gene expression studies have confirmed
that soluble starch synthase is a rate-
limiting step for grain filling in wheat when
exposed to high temperature (Hurkman et
al., 2003), while surprisingly no clear role for
heat shock proteins has been identified in
cereals despite a well-established role in
acclimation to heat stress in Arabidopsis
(Barnabas et al., 2008). Favourable water
relations are a crucial aspect of adaptation
to both drought and heat stress so further
understanding of the role of aquaporins,
which show a high degree of diversity, in
maintaining plant function under stress may
lead to useful genetic modifications
(Kaldenhoff et al., 2008). When combining
heat and drought stress, novel metabolic
responses have been demonstrated compared
to when stresses are experienced in isolation
(Mittler, 2006). Readers are referred to
comprehensive reviews of genomic
approaches to determine the mechanistic
basis of adaptation to heat and drought
stresses, which shed light on candidate genes
for crop improvement, by Chaves et al.
(2003), Shinozaki and Yamaguchi-Shinozaki
(2007) and Barnabas et al. (2008) and refer-
ences therein.
Part of the molecular basis for heat
susceptibility in wheat seems to be related
to ethylene levels. In a comparison of heat-
susceptible versus -tolerant winter wheat
cultivars, an increase in ethylene was shown
to be directly responsible for regulating the
heat-induced grain abortion and reduction
in kernel weight (Hays et al., 2007a).
Ethylene may be playing a fundamental role
in stress signalling, given that the ethylene
receptors share significant homology with
two-component histidine kinase receptors
in prokaryotes that have been shown to act
as heat sensors. However, ethylene-induced
kernel abortion and premature maturation
in response to heat stress, while possibly
being a useful survival trait (to temper prog-
eny load in warm, dry climates), is clearly
detrimental to productivity, and these stud-
ies have led to markers for selection against
its expression.
However, the general current under-
standing of the complex interaction of cellu-
lar/molecular mechanisms with whole-plant
adaptation to contrasting environments
does not yet permit its reliable application
in cultivar selection. Nevertheless, a few
ambitious projects exist, such as the C4 rice
initiative which aims to identify all of the
genes necessary to introduce Kranz anat-
omy and CO2-concentrating mechanisms
into C3 species (Hibberd et al., 2008), and
genetic modifications associated with
increasing CO2 fixation rate by Rubisco
(Parry and Hawkesford, Chapter 8, this
volume). If successful, these would lead the
way to substantial increases in heat adapta-
tion in C3 crops, as well as adaptation to
moderate levels of moisture stress, though
C4 photosynthesis is possibly more sensi-
tive to dehydration stress than is C3 photo-
synthesis (Ghannoum, 2009). On the other
hand, empirical studies involving geneti-
cally mapped populations have identified
quantitative trait loci (QTLs) associated
with adaptation to drought and heat; the
potential of these QTLs to achieve genetic
gains in yield is discussed later.
Breeding Approaches for Heat and
Drought Adaptation
Conventional breeding approaches have had
considerable impact in marginal environ-
ments as well as favourable ones. For exam-
ple, economic analysis shows that in the late
1990s, around 25% of global wheat produc-
tion increase came from improved produc-
tion in marginal environments (Lantican et
al., 2003). Much of this impact was achieved
by combining genes of major effect associ-
ated with agronomic type, phenology and
disease resistance into good yielding back-
grounds. However, impacts have also been
achieved more recently through targeting
specific heat- and drought-adaptive traits in
cereals. These have typically occurred for
integrative traits, such as transpiration effi-
ciency and canopy temperature (CT), which
are composite measures of numerous physio-
logical and morphological processes.
 Breeding for Adaptation to Heat and Drought Stress 79
Wheat breeding
Over 200 million ha of wheat are cultivated
worldwide in environments ranging from
very favourable in Western Europe to
severely stressed in parts of Asia, Africa and
Australia.
Breeding for dry environments in Australia
In Australia, trait-based breeding has
resulted in the adoption of a number of
useful traits affecting water-use efficiency.
These include intrinsic transpiration effi-
ciency of leaves as well as longer coleoptiles
and tillering traits that improve early season
canopy coverage and, therefore, decrease
surface water losses in environments with
early season moisture followed by post-
anthesis stress (Richards, 2006; Rebetzke et
al., 2009). A recent review of this research
(Rebetzke et al., 2009) emphasized the
opportunities to employ multi-disciplinary
approaches to develop improved wheat culti-
vars that have characteristics that modify
their water demands over the season (modi-
fications in vigour, tillering and canopy
structure) and their capability to maintain
water supply. For wheat, which is subject to
a large range of root stresses due to both
biotic (nematodes, Fusarium spp.) and
abiotic (salinity, B toxicity, Zn deficiency)
constraints, breeding for tolerance to such
conditions has resulted in favourable returns
in marginal environments even where aver-
age yields may be < 1.5 t/ha.
Breeding for dry environments internationally
The semi-dwarf habit – associated with Rht
genes – increased yield potential in all wheat
growing environments (Lantican et al.,
2003), sparking off the Green Revolution led
by Norman Borlaug, and led to the establish-
ment of international crop breeding insti-
tutes such as the International Maize and
Wheat Improvement Center (CIMMYT) and
the International Rice Research Institute
(IRRI), with IRRI leading the Green Revolu­
tion in rice. To this day, CIMMYT coordi-
nates an international collaborative wheat
improvement network that distributes
approximately 1000 new genotypes annu-
ally to collaborators worldwide (Braun et al.,
Chapter 7, this volume). These genotypes
are specifically targeted to the range of
mega-environments (MEs) found in wheat-
producing developing countries, including
MEs designated as experiencing substantial
periods of drought and heat. Analyses of
CIMMYT international yield trial data for
germplasm distributed to semi-arid envir-
onments between 1979 and 1998 (namely
of the Semi-Arid Wheat Yield Trial, SAWYT)
indicate highly significant genetic gains for
yield (Trethowan et al., 2002). Economic
analysis of the impact in drought- and heat-
affected environments showed annual yield
gains of 2–3% in the same period, in part
because it coincided with the first introduc-
tions of disease-resistant, semi-dwarf culti-
vars for many farmers in these more marginal
environments (Lantican et al., 2003).
However, the upward trend (~1%/year)
continues to the present for bread wheat
(Y.  Mannes, Mexico City, 2009, personal
communication), while durum wheat culti-
vars show still larger genetic gains of
1.2–1.4%/year (average increase for the
period 1983–2004) across hundreds of
environments worldwide (Fig 5.2). Although
the greatest progress is observed in the
drought-stressed sites, the data of Ammar et
al. (2008) clearly show that breeding for
broad adaptation has substantial impact
across a wide range of environments.
The CIMMYT approach focused initially
on delivering broadly adapted germplasm
that performed relatively well in dry years
but aimed to retain yield potential in above-
average rainfall years and where irrigation
was available. Subsequently, broader genetic
bases were utilized, including wild wheat
ancestors through wide crossing techniques,
generating re-synthesized hexaploid wheats
(Trethowan and Mujeeb-Kazi, 2008). This
provides genetic sources that can, for exam-
ple, confer more drought-adaptive root
growth to permit access to water from
deeper soil profiles (Reynolds et al., 2007).
Marker assisted selection (MAS) has also
been incorporated into conventional breed-
ing to screen for a number of genetically
simple traits mainly associated with disease
80 M.P. Reynolds et al.

160 <2.5 t/ha (Drought environments) Y = 1.40x – 2663. R 2 = 0.42

150
2.5–5.0 t/ha (Intermediate envs) Y = 1.32x – 2517. R 2 = 0.65
Yield (%) of adapted check

140
>5.0 t/ha (High yield envs) Y = 1.24x – 2369. R 2 = 0.75

130

120

110

100

90
1980 1985 1990 1995 2000 2005
14th–35th International Durum Yield Nursery (year)

Fig. 5.2.  Relative performance of the five top lines of the 14th–35th International Durum Yield Nursery
expressed as percentage yield of the widely adapted check cultivar ‘Yavaros 79’, grown at 827
environments in 48 countries between 1983 and 2004. Performance is expressed for three main
environments based on average nursery yield: < 2.5 t/ha, representing water-stressed sites ();
2.5–5.0 t/ha, (); and > 5.0 t/ha, representing well-watered sites () (figure drawn by Karim Ammar
using data from Ammar et al., 2008).

resistance (William et al., 2007). For exam- populations have facilitated gene discovery
ple, use of molecular markers for resistance for potential applications in molecular
to cereal cyst nematode improved the devel- breeding.
opment of healthy roots in the many low
rainfall areas where this pest is most prob-
Breeding for hot, dry environments
lematic (Nicol and Rivoal, 2007).
Physiological breeding approaches have Considerably more effort has gone into
also been recently adopted by CIMMYT and breeding crops for drought than for heat
are used in several phases of breeding adaptation. None the less, work in a few
(Reynolds et al., 2009). Specifically: (i) physi- heat-stressed environments has revealed
ologically characterized parents are used to valuable traits. The Southern Great Plains of
design crosses more strategically, thereby the USA are among the most challenging
resulting in cumulative gene action in environments for wheat cultivation and it
selected progeny; (ii) early generation selec- has been estimated that wheat loses 30–50%
tion – using high-throughput screening tools of its yield potential due to high tempera-
such as infrared thermometry – enrich the tures alone based on a yearly average
gene frequency for desirable traits before temperature of 28°C during reproductive
yield testing is feasible; (iii) evaluation of development (Hays et al., 2007b). The
non-adapted genetic resources – such as response of wheat to both chronic heat
landraces or even wild species – help deter- stress (Wardlaw et al., 1989) and short-term
mine genotypes that show promising expres- heat shock (Hays et al., 2007a) is well docu-
sion of stress-adaptive traits for subsequent mented and many of the current hard red
use in hybridization; and (iv) design and winter wheat varieties grown in the Great
precision phenotyping of experimental Plains region have shown susceptibility in
 Breeding for Adaptation to Heat and Drought Stress 81
terms of their inability to maintain yield and
quality under high temperatures (Hays et al.,
2007b). While varieties that show improved
yield stability under heat stress have been
identified (Hays et al., 2007a, b), the quanti-
tative nature of heat tolerance and unpre-
dictability of heat stress in the field make it
particularly difficult for breeders to effec-
tively select for the trait. Furthermore, in a
rainfed environment, heat is often exacer-
bated by drought stress (Mittler, 2006).
One trait that is showing promise in this
complex and unpredictable environment is
leaf glaucousness. As the primary interface
between the plant and the environment, the
plant wax cuticle is one plant adaptation
that can ameliorate both water loss from
epidermal transpiration and excess radia-
tion load. The cuticle reduces transpirational
cooling needs by acting as an adaxial and
abaxial reflective surface to excess light
energy. A reduced absorption at visible and
near-infrared wavelengths due to enhanced
reflectance can reduce internal tissue
temperatures and the vapour pressure differ-
ences between the tissues and the outside
air, which reduces transpirational water loss
(Sheppard and Griffiths, 2006). It has been
postulated that plants adapted to hotter,
dryer climates have thicker cuticles and
lower rates of transpiration through the
cuticle. In structurally similar leaves, when
stomates are closed, water loss has been
shown to be inversely proportional to the
cuticle thickness (Jenks et al., 1994). Despite
the apparent diversity in leaf wax layers and
the variation in wax composition, little criti-
cal information exists relating this variation
to improve adaptation under heat- or
drought-stress conditions. In wheat and
other cereals, epicuticular wax imparts a
bluish-green cast, and is a useful marker for
selecting for heat and drought adaptation.
Using pairs of near-isogenic lines of wheat,
Johnson et al. (1983) reported that leaf
waxiness reduced transpiration and
increased yield and water-use efficiency in
dryland conditions. Others have reported
similar effects, for example in rice
(Wassmann et al., 2009). Stem and leaf
cuticular wax is genetically simple. In wheat,
the gene for waxiness W1 has been mapped
to chromosome 2BS while a gene for heavy
wax is located on chromosome 2A
(Tsunewaki and Ebana, 1999).
Breeding for hot, irrigated environments
Considering germplasm targeted for warmer,
irrigated environments, analysis shows
significant progress in CIMMYT inter-
national nurseries, with many of the lines
that perform well at the hottest sites also
expressing good yield potential under more
temperate conditions (Lillemo et al., 2005),
an important consideration given typical
year-to-year variation in temperature. In hot
low RH environments, CT measured at the
breeding location was shown to be a good
predictor of performance across a range of
heat-stressed target environments (Reynolds
et al., 1994). More recent efforts have
focused on breeding for earlier maturing
cultivars that escape terminal heat stress
and encompass resistance to diseases associ-
ated with warm humid environments (Joshi
et al., 2007) as well as the highly virulent
Ug99 stem rust strain.
Selecting for root characteristics using
canopy temperature (CT)
Capacity for more extensive roots is an adap-
tive trait with good potential to increase
productivity in drought- and heat-prone
environments where water is available at
deeper soil profiles. For example, subsoil
water accessed during grain filling is used
especially efficiently since it contributes
entirely to grain growth (Kirkegaard et al.,
2007). While estimating root characteristics
of cultivars is not practical on a breeding
scale, measuring CT of crops permits rela-
tive water-uptake capacity by roots to be
estimated very easily. A repeatable value of
CT can be measured in about 10 s per plot
using an inexpensive infrared thermometer.
Validation studies using genetic resources
have shown that CT measured during peak
stress periods is associated with approxi-
mately 50% of the variation in soil water
extraction in soil profiles below 60 cm
82 M.P. Reynolds et al.
(Reynolds et al., 2007) and is directly associ-
ated with root depth (Lopes and Reynolds,
2010). CT measurements in a wheat popula-
tion of 167 recombinant inbred lines
confirmed the potential for achieving signif-
icant genetic gains when using CT as an
in­direct selection criterion; it typically
explains 50% or more of yield variation
under drought (Olivares-Villegas et al., 2007)
and heat stress (Amani et al., 1996; Pinto et
al., 2010). Economic analysis has confirmed
the value of CT as an indirect selection tool
to increase breeding efficiency (Brennan et
al., 2007) and several QTLs for CT have been
recently identified (Pinto et al., 2010).
Maize breeding
Maize is grown on approximately 150 million
ha worldwide, of which ~100 million ha is in
developing countries, though the latter
account for less than half of total produc-
tion. Over the last 100 years, maize has been
the major commercial success of cereals.
Adaptation of the crop in the main produc-
tion areas of the USA is now expanding
further into the more marginal western
areas (Mason et al., 2008), while production
and adoption of hybrids has also begun to
increase more rapidly in tropical regions,
particularly in Brazil, Argentina, India,
Thailand, Vietnam and parts of China.
Campos et al. (2006) demonstrated that the
major gains in productivity since the mid-
1950s have been in an increased tolerance to
stress. At low plant densities (< 20,000
plants/ha), modern hybrids have little
advantage over mid-20th century hybrids.
However, at higher commercial densities
and under conditions of drought (Campos et
al., 2006) and heat (Mason et al., 2008)
modern hybrids are better able to initiate
and establish productive ears and grains. Lee
and Tollenaar (2007) concluded that the
success of maize breeding was realized
through continuous and simultaneous
improvements in the maintenance of the
‘source’ of assimilate supply, mainly through
increased stay-green (under conditions
including stress), and in the ‘sink’ as
described below.
Maize is relatively well adapted to high
temperature and also shows good transpir-
ation efficiency because of the C4 character-
istic of concentrating CO2 to bypass the
oxygenase activity of Rubisco. However,
maize shows large genetic variation in the
relative timing of male and female flower-
ing, commonly referred to as the anthesis–
silking interval (ASI). Since expression of
longer ASI is associated with significantly
larger relative investment in tassel biomass
over ear biomass (and under extreme stress
may result in total ear barrenness while not
preventing pollen dissemination), delayed
ASI leads to reduced kernel set under
drought and a number of other stresses
(Edmeades et al., 2000). Based on this, ASI
was used as the main physiological selection
criterion to make genetic gains under
drought in CIMMYT’s maize stress breeding
programme (Edmeades et al., 2000). Building
on ASI-improved germplasm and the concept
of selection under well-managed stress
environments, Bänziger and colleagues
(2006) began a maize breeding programme
in CIMMYT’s sub-Saharan Africa operation
in 1997 that has resulted in dozens of new
hybrids which, on average, outperformed
standard checks (checks are well-adapted
elite cultivars) across a broad range of envir-
onments at over 40 locations across eastern
and southern Africa – and by as much as
100% under severe stress.
Sorghum breeding
Sorghum, which is grown on approximately
40 million ha worldwide, is an especially
important crop for resource-poor farmers in
rainfed regions of the developing world as a
result of its excellent level of adaptation to
drought and heat stress (again related to its
C4 metabolism) and its dual-purpose nature,
it being used both in cooking and, as the
stover, for animal feed.
Maintenance of stay-green under termi-
nal drought conditions is used as a visual
 Breeding for Adaptation to Heat and Drought Stress 83
selection criterion for sorghum breeding
under drought in the USA and Australia
(Borrel et al., 2000 and references therein).
Stay-green is valuable not only as a selection
criterion for yield under drought but also
because non-senescent genotypes accumu-
late more soluble sugars in stems during and
after grain filling to improve nutritional and
commercial value (McBee et al., 1983).
Research has suggested that greater green
leaf area duration in sorghum is the product
of different combinations of three factors:
green leaf area at flowering, time of onset of
senescence and rate of senescence, all of
which appear to be inherited independently
(Borrell et al., 2000; Borrell and Hammer,
2000).
Despite the ease with which stay-green
can be selected, a number of doubts have
existed among breeders with respect to its
merits, including: (i) whether the trait might
be associated with smaller panicle size; (ii)
that its selection under drought might result
in a yield penalty under irrigated conditions;
(iii) the magnitude of genetic gains associ-
ated with its selection; and (iv) whether it is
also involved in lodging resistance. These
issues were comprehensively addressed by
Borrell and colleagues (2000) in a study of
nine closely related hybrids that varied in
rate of leaf senescence under contrasting
water regimes in north-eastern Australia.
While differences in yield among hybrids
under well-watered conditions were negligi-
ble, under terminal water stress stay-green
hybrids produced almost 50% more post-
anthesis biomass than senescent lines, and
green leaf area at maturity was strongly
correlated with grain yield (Borrell et al.,
2000). Mechanisms related to supply and
demand for N during grain filling contribute
to stay-green expression in sorghum and
include: (i) a higher initial level of leaf N at
flowering; (ii) more N uptake during grain
filling; (iii) less remobilization of N from
leaves; and (iv) larger retention of chloro-
plast proteins until late senescence (Borrel
and Hammer, 2000). Genetic studies have
identified QTLs associated with stay-green
(Harris et al., 2007).
Rice breeding
Rice, which is grown on ~150 million ha
worldwide, is the major staple food in Asia,
where 90% of the crop is produced. IRRI
leads an Asia-based rice research and breed-
ing programme which tackles all aspects of
adaptation including to drought and heat
stress. While most rice is grown under
monsoonal rains, a substantial area is also
grown under dryland conditions with the
possibility of water deficit. Evolving from a
semi-aquatic ancestor, rice is generally more
susceptible to water-limited conditions
compared to other cereals crops (Wassmann
et al., 2009). None the less genetic variation
has been exploited and under upland field
conditions, increased root diameter, and
depth and/or branching of root systems
have been associated with decreased plant
water stress and increased grain yield under
severe stress (Lafitte and Courtois, 2002).
QTLs associated with constitutive and adap-
tive root growth under drought have been
identified (Khowaja et al., 2009). As proof of
concept, near-isogenic lines (NILs) were
developed by introgressing four root QTLs
on chromosomes 2, 7, 9 and 11 from the
variety Azucena into the Indian upland vari-
ety Kalinga III, and evaluated in the field and
on-farm trials; NILs with root QTLs out-
performed Kalinga III for grain and straw
yield (Steele et al., 2007).
Under drought stress, decreased pedun-
cle elongation reduces panicle extrusion and
florets that remain in the flag leaf sheaf are
usually completely sterile, severely reducing
grain yield in cultivars that are prone to
reduced extrusion (O’Toole and Namuco,
1983). Selection for continued peduncle
elongation under reproductive stage drought
stress in rice is being used to increase grain
yield under field drought stress. Rice pedun-
cle elongation is partially controlled by local
gibberellin levels (Kaneko et al., 2004).
Repression of cell-wall invertase genes and
the cell-wall loosening genes for xyloglucan
endotransglycosylase/hydrolase (XTH) have
also been linked to reduced peduncle elong-
ation (Ji et al., 2005).
84 M.P. Reynolds et al.
Comparatively less research has been
conducted on heat tolerance in rice
(Wassman et al., 2009). Genetic variation
for high temperature tolerance per se has
been observed in rice, with flowering being
the most sensitive stage. Variation for the
time of day of flowering is an important
mechanism of heat avoidance (Jagadish et
al., 2008). Oryza glaberrima flowers earlier in
the day than Oryza sativa and crosses
between them have shown that earlier flow-
ering can be easily selected for (Prasad et al.,
2006).
For further details on breeding of cereals
for adaptation to low-yielding stress envir-
onments, readers are referred to chapters in
Drought Adaptation in Cereals (Ribaut,
2006).
Strategies to Accelerate Genetic
Gains
Outputs from the above examples, while
providing stress-adapted genetic stocks, also
serve as good models for breeders and
researchers worldwide tackling drought and
heat stress. The following section will focus
on other promising approaches that are
likely to have additional impacts in the near
future.
Exploration of genetic resources to boost
physiological and molecular breeding
While conventional plant breeding has
already achieved significant progress in
stress breeding as outlined, three main
approaches can be employed to widen gene
pools: (i) introgression of traits from genetic
resources with compatible genomes, such as
landraces; (ii) wide crosses involving inter-
specific or intergeneric hybridization; and
(iii) genetic transformation. To date genetic
resources have been used mainly to intro-
duce resistance to biotic stresses (Dwivedi et
al., 2008), while relatively few wild crop rela-
tives have been exploited for adaptation to
abiotic stress (Hajjar and Hodgkin, 2007). In
fact, the majority of accessions in germ-
plasm collections remain uncharacterized in
terms of their potential to improve yield
under abiotic stress; current challenges are
to identify elite sources of traits among
genetic resources, estimate potential yield
gains associated with trait expression in
good agronomic backgrounds, and define
potentially complementary traits that if
introgressed into a common genetic back-
ground are likely to result in cumulative gene
action for yield (Reynolds et al., 2009).
Hexaploid wheat has been a useful model for
alien introgressions and impacts include
increased yield in a range of environments
including drought (Trethowan and Mujeeb-
Kazi, 2008). Another avenue currently being
explored is the use of Leymus racemosus to
introgress genes for root exudation of nitri-
fication inhibitors (Subbarao et al., 2007);
the potential impact on reducing potent
greenhouse gas emissions is enormous and
could significantly mitigate global warming
if successfully adopted on a global scale. A
vast reserve of genetic potential in closely
related crop species has yet to be evaluated,
and as understanding of the physiological
and genetic basis of stress adaptation
improves, it will become easier to apply
molecular marker technology to mine
genetic resource collections for potentially
useful alleles.
Transgenic technology effectively
re­moves taxonomic barriers altogether but
although much data has been collected under
controlled environments for candidate genes
that improve survival of both model and
crop species under abiotic stress (Umezawa
et al., 2006), more candidate genes need to
be tested in a range of relevant field environ-
ments (Nelson et al., 2007) if impacts are to
be achieved. Candidate genes, such as those
associated with functional proteins and
especially upstream regulation, could affect
any of the drivers of yield under stress (see
Fig. 5.1 for examples) depending on at what
stage of development and in which tissue
they are expressed. One well-studied candi-
date gene is DREB1A; stress-regulated
expression of this gene with the rd29A
promoter produced plants with increased
tolerance to freezing, salt and drought
 Breeding for Adaptation to Heat and Drought Stress 85
stresses, without producing changes in the
normal phenotype of the transformed plants
(Chandler and Robertson, 1994). The gene
has been associated with improved root
growth under water stress in well-controlled
phenotyping studies in groundnut (Vadez et
al., 2007). Another approach that may be
useful in tackling climate change is to replace
genes that are especially heat susceptible in
temperate crops with their analogues from
tropical species like rice or maize; a good
example would be soluble starch synthase
which is a rate limiting step to grain filling in
wheat at high temperature (Hurkman et al.,
2003).
Molecular breeding for drought and heat
In breeding applications, molecular markers
may be either diagnostic (i.e. perfect mark-
ers of a specific allele within a specific gene
sequence) or putative (e.g. markers associ-
ated with or flanking a QTL that has been
discovered via mapping in biparental crosses
or in association panels of related or unre-
lated lines). Diagnostic markers are prefer-
able as they can be used to select desired
alleles in any parental or progeny line of a
species under any crossing strategy.
Alternatively, such markers can be used to
prepare a gene for transgene (genetic modifi-
cation, GM) approaches within or across
crop species. QTL markers from mapping
studies are not perfectly linked to genes (i.e.
they are ‘nearby’) and are frequently difficult
to transfer between crosses, unless there is
substantial research investment in crossing
and mapping to ‘fine map’ the QTL to locate
markers that are within a gene. The identifi-
cation of QTLs for complex traits is further
confounded by substantial genotype × envir-
onment interaction effects that occur for
traits like heat and drought adaptation.
Crossa et al. (Chapter 14, this volume) high-
light the new capabilities in statistical
methods­, such as modelling of QTL × envir-
onment effects (Boer et al., 2007) that enable
the more robust detection of useful genomic
regions for selection.
MAS is routinely applied for traits such as
disease resistance and grain quality
characters­ when diagnostic gene-based
markers have been identified (William et al.,
2007; Whitford et al., Chapter 12, this
volume). Such markers, located within a
gene sequence, are discovered through either
fine mapping around QTLs of large effect, or
by looking for gene candidates that are part
of known pathways (e.g. functional disease
resistance genes). Only few QTLs of large
effect have been documented for perform-
ance-related traits under heat or drought
and no candidate genes in known biochem-
ical pathways of response to heat or drought
have been shown to have large effects on
performance traits such as yield. Using fine-
mapping approaches, genes have been iden-
tified and cloned for a number of abiotic
stresses, including salinity, flooding, Al
tolerance and B tolerance (Collins et al.,
2008), but none has been cloned from QTLs
associated with drought or heat stress. In
part, the low success rate for these stresses
relates partly to the genetic and environ-
mental complexity of adaptation. Mapping
populations have frequently been made by
crossing highly contrasting parents to maxi-
mize genetic polymorphisms in the progeny.
Therefore, performance QTLs identified in
random lines or in deliberately contrasting
lines are likely to be associated with traits
that have already been optimized by breed-
ing. Furthermore, in crops like wheat and
barley, it has been demonstrated that segre-
gation for genes of major agronomic effect
(height and maturity) within experimental
populations makes it more difficult to iden-
tify QTLs of minor effect that may be associ-
ated with more direct mechanisms of
adaptation (Reynolds et al., 2009). Using
mapping populations with more uniform
flowering time (Olivares-Villegas et al.,
2007) both trait and yield QTLs were readily
detected independent of loci associated with
phenology (Pinto et al., 2010).
Discovery and utilization of QTLs for
drought and heat tolerance requires further
investment in development of genetic
resources and in more detailed phenotypic
‘dissection’ of complex performance traits.
86 M.P. Reynolds et al.
To assist with gene discovery, several preci-
sion phenotyping protocols based on remote
sensing can be applied, including spectral
reflectance indices for a range of growth-
related parameters (Montes et al., 2007) and
infrared thermometry as mentioned earlier.
Application of these principles in wheat has
led to the identification of a number of QTLs
that are associated with both drought and
heat adaptation, which suggests some
common genetic basis for adaptation to
these two stresses (Pinto et al., 2010). The
usefulness of such traits in selection requires
the development of a comprehensive under-
standing of the genetic and environmental
influences that determine their effect on
yield and other performance characteristics
(see Crossa et al., Chapter 14, this volume).
Molecular breeding is benefiting from the
rapidly decreasing cost of genotyping, and
points to a more pragmatic future in which
phenotyping is again highly valued.
Commercial breeding programmes (espe-
cially in maize and soybean) are now begin-
ning to release germplasm that has been
developed for yield through the application
of marker-assisted recurrent selection
(MARS) (Eathington et al., 2007). This
approach relies on cheap abundant marker
systems being applied to a large number of
accurately phenotyped biparental popula-
tions, followed by rigorous statistical meth-
ods. Breeders either estimate QTLs using
the types of methods described by Boer et al.
(2007) or apply techniques such as genome-
wide selection (GWS) to assign predictive
values to every marker used in the analysis
(e.g. Heffner et al., 2009). Favourable QTLs
and/or markers are then used in several
cycles of glasshouse selection to quickly
assemble new inbred lines as complexes of
useful genomic regions, although without
direct knowledge of the genes or their mech-
anisms (i.e. fine mapping and gene discovery
is not utilized at all in the breeding, although
these may follow at a later date to locate
genes for future use as diagnostic markers or
in gene transformation). Heffner et al.
(2009) have argued that the typical lack of
success in breeding with QTLs means that
genome-selection methods, where every
marker has a value (positive or negative),
will probably take over from QTL approaches.
MARS molecular breeding methods acceler-
ate the traditional phenotyping approach of
breeding and are being deployed in many
breeding programmes as an adjunct to
phenotypic methods. Readers are referred to
the chapter by Whitford et al. (Chapter 12,
this volume) for further examples of applica-
tions of biotechnology in breeding.
Conclusions
In terms of genetic improvement of crops, a
number of research approaches can be
adopted to help offset the negative effects of
climate change. Multi-disciplinary breeding
with a special focus on adaptation to warmer
and drier environments should be the base-
line. New genetic variation can be introduced
into such programmes, for example, through
interspecific hybridization with crop rela-
tives, or by introducing genes of proven value
from model species. Thorough characteriza-
tion of target agroecosystems is essential
such that different models of genetic adapta-
tion can be systematically evaluated, taking
into account climatic and edaphic factors as
well as management practices. A more
complete understanding of the environment
will also help with gene discovery and deploy-
ment of QTLs for complex adaptive traits.
Application of appropriate tools – molecular
techniques, remote sensing for precision
phenotyping, networks of field operations,
etc. – will permit rapid genome analysis to be
coupled to the adaptive response of crops.
Determination of the theoretical limits to
yield under water-limited and temperature-
stressed environments will help to establish
realistic research targets, while new research
must consider how crops can maintain
productivity in warmer climates without
substantial sacrifices in water-use efficiency,
as well as adapt to extreme climatic events
such as sudden temperature spikes and
combinations of stresses. Given that climate
is in a state of flux, more extreme weather
variation can be expected in the future,
therefore new ideotypes should be evaluated
for their relative yield stability, using realistic
farmer conditions, under a full range of
 Breeding for Adaptation to Heat and Drought Stress 87
potential scenario­s from optimal, well-
managed en­­­­vir­on­ments to those with
extreme climatic stresses.
Acknowledgements
MPR acknowledges Jill Cairns for providing
information on rice breeding and the
Australian Grains Research and Develop­
ment Corporation (GRDC) for its financial
support. SC leads the project ‘A national
research programme for climate-ready
cereals’ funded by the Department of
Agriculture, Fisheries and Forestry under
Australia’s Farming Future: Climate Change
Research Program.
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 6
Breeding Crops for Tolerance to
Salinity, Waterlogging and
Inundation

Daniel J. Mullan and Edward G. Barrett-Lennard

Abstract
During the next century, global climate change is likely to cause substantial increases in the severity
with which salinity, waterlogging and inundation affect crop production in many of the world’s
agricultural regions. In this chapter we address the effects of climate change on these three
environmental stresses in terms of their threat to sustainable crop production. The effects of salinity,
waterlogging and inundation on crop plants are examined, with a focus also directed towards the
exacerbating effects of the complex interactions between these stresses. We identify key plant
physiological traits as targets for breeding initiatives. Three possible approaches to the development
of crops for saline, waterlogged and inundated soils are considered: (i) selection within crop species;
(ii) the development of hybrids between adapted wild species and crop plants; and (iii) the domestication
of halophytes. Finally, we detail some of the complex research, development and agricultural issues
that need to be addressed by a broad research and development community in order to increase crop
production during the foreseeable period of global climate change.

Introduction subtropical land regions, and future tropical

storms will become more intense (IPCC,
Climate change is expected to have a variety 2007). One of the large unknowns is the
of effects on global temperatures, sea levels extent to which the melting of the Greenland
and the availability of water in agricultural and Antarctic ice sheets will impact on sea-
landscapes. According to the Intergovernmen­ level rise. The 2007 IPCC report notes that
tal Panel on Climate Change (IPCC), since the expected future temperatures in
1950 average global surface temperatures Greenland are comparable to those inferred
have risen by ~0.7°C and the sea level has for the last interglacial period 125,000 years
risen by ~10 cm. There has also been decreased ago, when palaeological data suggest that the
precipitation in the Sahel, the Mediterranean, loss of polar land ice was associated with a
southern Africa and parts of southern Asia, 4–6 m rise in sea level (IPCC, 2007). Global
and an increased risk of heavy precipitation climate change is likely to invoke substantial
events over most areas (IPCC, 2007). changes to the world’s agricultural regions
Over the next century, average global and the severity with which abiotic stress
surface temperatures are expected to rise by will affect crop production.
1.8–3.5°C. As a consequence, the thermal Salinity is widespread, particularly in arid
expansion of the oceans will lift sea levels by regions (Ghassemi et al., 1995), and it can
up to 0.6 m, annual precipitation will increase coincide with the additional stresses of
in high latitudes and decrease in most waterlogging and periodic inundation1
1We prefer these separate terms to ‘flooding’, which is used ambiguously in the literature to refer to both
saturation of the soil (waterlogging), which affects roots (e.g. Barrett-Lennard, 2003; Colmer and Flowers,
2008), and the covering of shoots with water (inundation), which affects both shoots and roots (e.g.
Pedersen et al., 2006).
92 © CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds)
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 93
(Barrett-Lennard, 2003). In these cases the
combination of salinity, waterlogging and
inundation may be of natural origin, linked
with proximity to waterways, lakes and flood
plains (primary salinity), or it may have an
anthropomorphic origin (secondary salin­
ity). In the latter cases, the agricultural vege­
tation uses less than the incident rainfall (or
irrigation water), excess water percolates
into the soil profile, the water table rises
towards the soil surface, and where the
groundwater comes to within ~2 m, salt rises
to the soil surface through capillarity
(Ghassemi et al., 1995). The total area of
secondary salinity around the world has
been estimated at ~76.6 million ha (Table
6.1), though this is almost certainly an
underestimate, being based on data acces­
sible in 1991.
Although it has been long recognized that
salinity can occur in landscapes associated
with a shallow water table (e.g. Wood, 1924),
understanding the implications that the
coincidence of salinity, waterlogging and
inundation have for plant growth is rela­
tively recent. Initial studies in the area
focused on the need to obtain useful produc­
tion on salinized irrigated land (see papers
by West and colleagues – cited by Barrett-
Lennard, 1986) and subsequent studies
focused more on the interaction between
salinity and moisture excess as a physio­
logical curiosity (reviewed by Barrett-
Lennard, 2003). More recent research has
examined the effects of the combined
constraints on the growth of saltland
pastures (reviewed by Bennett et al., 2009)
Table 6.1.  Global extent of human-induced salinization (reproduced from Ghassemi et al., 1995, p. 19
with permission from University of New South Wales; data from Oldeman et al., 1991).
Level of salinization (million ha)
Continent Light Moderate
Africa 4.7 7.7
Asia 26.8 8.5
South America 1.8 0.3
North and Central 0.3 1.5
America
Europe 1.0 2.3
Australasia – 0.5
Total 34.6 20.8
and the physiology of halophytic vegetation
(reviewed by Colmer and Flowers, 2008).
Climate change can be expected to have
varying effects (both negative and positive)
on the expression of salinity, waterlogging
and inundation in landscapes.
First, there will be increased irrigation
with hazardous water. Hydrological basins
are defined as being water stressed if they
either have a per capita water availability of
less than 1000 m3/year or they have a ratio
of withdrawals to long-term average annual
runoff above 0.4. Using these criteria, water-
stressed basins occur in northern Africa, the
Mediterranean region, the Middle East, the
Near East, southern Asia, northern China,
Australia, the USA, Mexico, north-east Brazil
and the south-west of South America. These
areas have a population of 1.4–2.1 billion
people (Bates et al., 2008). As areas at risk
become hotter and drier, good quality water
will increasingly be reserved for drinking
and urban use, and irrigators will turn to the
use of brackish water and water of high
sodium hazard. Irrigation with water of high
sodium hazard on fine textured soils leads to
soil sodicity (i.e. the decline of soil structure
associated with the substitution of Na+ for
Ca2+ in the soil’s cation exchange complex).
Under these conditions, there is a decreased
rate of infiltration, a lack of salt leaching and
the development of saline/waterlogging
stresses (reviewed by Qureshi and Barrett-
Lennard, 1998).
Secondly, there will be increased inunda­
tion in valley floors and low-lying landscapes
associated with increased runoff from
Strong Extreme Total
2.4 – 14.8
17.0 0.4 52.7
– – 2.1
0.5 – 2.3
0.5 – 3.8
– 0.4 0.9
20.4 0.8 76.6
94 D.J. Mullan and E.G. Barrett-Lennard
tropical­storms. The IPCC rates the probabil­
ity of a link between increased tropical storm
activity and global warming as ‘more likely
than not’. In the North Atlantic the 10-year
running average number of named tropical
storms has increased from ~10/year (1930–
1990) to ~15/year (1998–2007) (Pew Centre
on Global Climate Change, 2009). The effects
of climate change are likely to be especially
severe for regions in South Asia. The
frequency and severity of inundation are
expected to increase due to increased rain­
fall and temperatures. Monsoon rainfall is
expected to increase in magnitude and raise
the frequency and severity of inundation in
the Ganges, Brahmaputra and Meghna
basins (Douglas, 2009). Furthermore, higher
tem­pera­tures will increase the melting of
Himalayan snowfields and glacial ice, signifi­
cantly increasing the occurrence of inunda­
tion through greater river flows and extreme
weather events (Jagtap and Nagle, 2007;
Douglas, 2009). Inundation in landscapes at
risk of salinity will cause substantial
increases in recharge to the groundwater, a
rise in the water table and increased expres­
sion of salinity as the groundwater evap­
orates at the soil surface. The most acute
consequences of inundation can presently
be seen in Bangladesh, where nearly 85% of
the rainfall occurs during the monsoon
(June–October). High-intensity floods occur
when any two of the three major rivers reach
peak flow conditions simultaneously, and
over half of the country has an elevation
within 10 m of average sea level (Ahmad and
Ahmed, 2003). In this landscape, the return
period of severe floods is every 7 years
(Ahmad and Ahmed, 2003), and during the
1998 flood, about 70% of the country’s area
was inundated (compared to an average
value of 20–25%; Bates et al., 2008). Soil
salinity in the field is commonly measured
as the electrical conductivity of the satura­
tion extract (ECe). The coastal ricelands of
Bangladesh generally have a shallow water
table (~1.0–1.5 m below the soil surface) and
in the dry season soil salinity in the upper
15 cm of the soil profile varies from between
moderately (ECe = 4–8 dS/m) to highly saline
(ECe = 8–16 dS/m) (Mondal et al., 2001).
Thirdly, there will be adverse effects on
agricultural production and natural ecosys­
tems in landscapes at low elevations above
sea level. Coastal areas exposed to the future
rising sea level will be subject to an increased
risk of inundation from high tides and storm
surges, and from increased subsoil seawater
intrusion. Such areas include the world’s
river deltas, especially the Asian mega deltas
of the Ganges-Brahmaputra in Bangladesh
and West Bengal (Bates et al., 2008). Nicholls
(1995) predicts that an increase of 1 m will
inundate over 17% of Bangladesh. Clearly,
sea level rise will have major implications for
the severity of salinity, waterlogging and
inundation, future land use and the develop­
ment of more tolerant crops for the region.
However, not all the effects of climate
change on salinity, waterlogging and inun­
dation will be negative. In semi-arid envir­
onments there may be decreases in dryland
salinity associated with a decline in depth to
water table. In the south-west of Australia,
dryland salinity is caused by the replace­
ment of native vegetation with annual crops
and pastures; this has resulted in a general
rise in water table over the last 150 years,
and about 2.32 million ha have been
regarded as being at risk from dryland salin­
ity (Sparks et al., 2006). However, since
2000 the region has experienced a decline
in winter rainfall of about 20% (Bureau of
Meteorology, 2009), which has caused an
increase in depth to water table, decreasing
the area at risk of salinity, particularly in
the northern (drier) areas of the wheatbelt
(George et al., 2008).
This chapter has three main sections.
First, we examine the effects that salinity,
waterlogging, inundation and their inter­
actions have on crop plants and the traits
that plants need to withstand these effects.
Secondly, we consider three different
approaches for the selection of plants for
affected landscapes: (i) selection within crop
species; (ii) the development of hybrids
between adapted wild species and crop
plants; and (iii) the domestication of halo­
phytes. Finally, we conclude with some
thoughts about priorities for future
research.
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 95
Stresses and the Key Plant
Physiological Adaptations
Salinity
Soil salinity affects plant growth and survival
because ions (mainly Na+ and Cl–, but also
Ca2+, Mg2+ and SO42–; Richards, 1954)
increase in the soil solution to concentra­
tions that adversely decrease the availability
of water to the plant (the ‘osmotic effect’).
The accumulation of these ions in the plant
tissues also impairs plant metabolism and
growth (the ‘toxic effect’) (Greenway and
Munns, 1980). The effects differ in their
timing: the osmotic effects are immediate,
but the ion toxicity effects take time (days or
weeks) to decrease growth (Munns, 2002).
Figure 6.1 shows typical vegetative growth
responses for three species: river saltbush
(Atriplex amnicola; a typical halophyte),
barley (a salt tolerant crop) and beans (a salt
sensitive crop). Most crop species would
have economic yields only at soil ECe values
less than 10 dS/m.
The key physiological traits associated
with salt tolerance in crops centre around
factors that: (i) enable plants to withstand
the adverse water relations caused by salin­
ity; (ii) decrease the movement of toxic ions
100
Yield (% low salt)
50
0
0 10
Estimated EC e (dS/m)
Fig. 6.1.  Growth responses of young plants to salinity (Barrett-Lennard et al., 2003). We have assumed a
soil at field capacity salinized with NaCl (Richards, 1954).
to the shoots; and (iii) complete the life cycle
in the least saline part of the growing season
(Greenway and Munns, 1980; Munns, 2002;
Colmer et al., 2005). In relatively saline soils,
the traits of importance are:
• High Na+ (and Cl–) exclusion at the root
surface: this refers to the root plasma­
lemma having low permeability, the
uptake of Na+ being regulated by K+-
selective transporters and channels, and
the efflux of Na+ being regulated by Na+/
H+ antiporters (Colmer et al., 2005).
• High K+/Na+ discrimination: this refers to
the maintenance of K+ uptake even in the
face of very high Na+/K+ in the soil solu­
tion; these traits are also regulated by
K+-selective transporters and channels,
and effective efflux of Na+. This trait is
important because Na+ can compete with
K+ for uptake by the roots, and K+ is a
major osmoticum and macronutrient
that is essential for enzyme functioning.
• Ability to remove ions from the xylem
stream: this refers to the localizing of ions
into less damaging locations than leaves
(e.g. Cl– in leaf sheaths of sorghum –
Boursier et al., 1987; Na+ in stems of
beans – Jacoby, 1964; Na+ in leaf sheaths
of durum wheat – James et al., 2006).
River saltbush
Barley
Beans
20 30 40
96 D.J. Mullan and E.G. Barrett-Lennard
• Ability to tolerate ions in the tissues: this
refers to the ability of plants to effectively
compartmentalize Na+ and Cl– into cell
vacuoles where they have a lower chance
of interfering with the activities of the
enzymes involved in metabolism in the
cytosol and cellular organelles.
• Ability to adjust osmotically: this refers to
the accumulation of solutes in cells to
maintain cell turgor, and is achieved
through the compartmentation of ions
(particularly Na+ and Cl–) into vacuoles,
and the synthesis of organic solutes (e.g.
glycinebetaine and proline) that are
compatible with enzyme function, which
are located in the cytosol.
• Enhanced ability to accumulate Na+ and Cl–
in older rather than younger leaves.
• Enhanced vigour, and early flowering and
grain filling: this refers to the ability of
the plant to grow rapidly when condi­
tions are cool and soil water is more avail­
able, and the ability of the plant to
complete its life cycle before the salinity
of the soil solution increases at the end of
the growing season.
In addition to these traits, it is also neces­
sary for seeds to remain viable and germin­
ate in saline soils, and although genotypic
variation exists in the tolerance of seeds to
salinity (Ungar, 1978; Nichols et al., 2009),
the physiological traits associated with this
capacity are not known.
Some of the above traits are relatively
easy to assess. For example, Na+ and Cl–
exclusion and the discrimination between
K+ and Na+ can be assessed by measuring the
concentrations of ions in specific tissues
such as the youngest fully expanded leaf (as
recommended by Greenway and Munns,
1980). However, other traits can be harder
to assess. These include the ability to adjust
osmotically (which requires accurate meas­
urements of the change in relative growth
rate in the immediate few days after salinity
is applied) and the ability of plants to toler­
ate ions in the leaves (which requires meas­
urements of the degree of leaf senescence
specifically caused by salinity). The use of
non-destructive imaging systems to assess
plant growth over short time frames, and to
separate natural- from salt-induced senes­
cence in leaves may lead to greater progress
in the latter two areas (cf. Rajendran et al.,
2009).
Given the wide range of physiological
traits associated with tolerance to salinity, it
is not surprising that reviewers have
suggested that this tolerance requires the
involvement of a number (unknown) of
genes (Flowers and Yeo, 1995), and attempts
to improve the salt tolerance of crop plants
have only occasionally been effective (Colmer
et al., 2005; discussed further in the ‘Breeding
for Tolerance’ section).
Waterlogging
Waterlogging refers to saturation of soils by
water. This leads to the displacement of air
from the soil pores and an approximate
10,000-fold decrease in the rate at which O2
diffuses into the soil (Grable, 1966). As a
result, soils typically become hypoxic (O2
deficient) within a few days. Although soil
hypoxia has a range of moderate- to long-
term impacts on the chemistry and biology
of soils, the effects on plant roots are quite
rapid (see reviews by Ponnamperuma, 1972;
Drew and Lynch, 1980). Plants require O2 to
provide the energy for root growth and func­
tion; with O2 available, plants are able to
produce 24–36 moles of the energy storage
compound adenosine triphosphate (ATP)
per mole of glucose; without O2, plants are
only able to produce 2 moles of ATP per mole
of glucose through alcoholic fermentation.
Root-zone hypoxia has a variety of effects
on plant roots. Decreases in the elongation
of roots and the death of non-adapted apices
are observable within a few hours to a day
(Thomson et al., 1990), and this can lead to
substantial decreases in total root relative to
shoot biomass within 1 week. For example,
exposure of barley seedlings to 6 days of
hypoxia (O2 concentrations ~10% of satur­
ated) decreased the root:shoot ratio from
~0.37 (well aerated) to 0.23 (hypoxic) (calcu­
lated from data of Benjamin and Greenway,
1979). Hypoxia can decrease the uptake of
nutrients by crop plants (Trought and Drew,
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 97
1980; Buwalda et al., 1988) and, therefore,
transient waterlogging can decrease yields if
crops are not subsequently refertilized
(Robertson et al., 2009).
In addition to these effects, in water­
logged saline land, root-zone hypoxia can
lead to increased Na+ and/or Cl– uptake to
the shoots, which decreases plant growth
and survival (reviewed by Barrett-Lennard,
1986, 2003). In a wide-ranging review of the
literature, hypoxia under saline conditions
caused at least 30% increases in either Na+
or Cl– concentrations in the leaves or shoots
of 23 of 24 species surveyed (Barrett-
Lennard, 2003).
Waterlogging tolerance in crops is primar­
ily associated with two major physiological
traits that enable plants to avoid soil hypoxia.
The first of these is the formation of roots
with increased porosity in the cortex (aeren­
chyma) that enable O2 to be conducted down
the inside of the root from the root/shoot
junction to the root tip. The simplest method
for determining root porosity is using
Archimedes’ Principle: porosity can be calcu­
lated knowing the fresh weight of root
segments, and the weight of these segments
when suspended in water before and after
the evacuation of root air spaces under
vacuum (cf. Thomson et al., 1990). These
kinds of assessments show that the porosity
of a plant’s roots is partly constitutive (i.e.
relating to the habitat in which plant natur­
ally occurs, plants from moist habitats
generally having higher porosities than
plants from well-drained habitats), and is
partly inducible (i.e. relating to the current
growth conditions, plants growing under
waterlogged conditions generally having
higher porosities than plants growing under
drained conditions). This principle can be
illustrated using data from a survey of 91
plant species conducted by Justin and
Armstrong (1987) (Fig. 6.2). In this survey,
plants collected from perpetually inundated
landscapes (H1) had root porosities (95%
confidence interval) of 16–29% when grown
under drained conditions, and 25–36% when
grown under waterlogged conditions,
whereas plants collected from well-drained
habitats (H5) had root porosities of only
1–10% when grown under drained condi­
tions, and of 4–15% when grown under
waterlogged conditions.
The role of increased root porosity in
helping to maintain root growth can be seen
in a data set based on an assessment of the
effects of hypoxia on ten species from the
tribe Triticeae (McDonald et al., 2001). In
this work, there were significant relation­
ships between the porosity of adventitious
roots under stagnant conditions and: (i) the
ratio of adventitious root dry mass to shoot
dry mass; and (ii) the maximum length to
which these roots grew under stagnant
conditions (Fig. 6.3). These results are
consistent with the view that under hypoxic
conditions, the growth of the root apex
becomes limited by the availability of O2
supply to the root tip; therefore, plants with
higher porosity develop more roots and
longer roots (cf. Armstrong, 1979).
The second physiological adaptation crit­
ical for plant growth in waterlogged soils is
an ability to form a barrier to radial oxygen
loss (ROL) that decreases the leakage of O2
out of the root, so that more O2 can diffuse
internally and reach the root tip (Armstrong,
1979; Jackson and Armstrong, 1999;
Colmer, 2003). The presence of a barrier to
ROL is inferred from rates of radial oxygen
flux from roots, which is measured using
root-sleeving cylindrical Pt electrodes that
are moved up and down the root to deter­
mine rates of O2 flux at different distances
from the root tip. Colmer (2003) categorizes
the barrier to ROL as falling into three
general classes: (i) a ‘tight’ barrier is indi­
cated by very low ROL from expanded zones
of the root, but high rates near the root tip;
(ii) a ‘partial’ barrier results in similar rates
of ROL along the root; and (iii) a ‘weak’
barrier results in the ROL being much higher
in the expanded zones of the root compared
with the root tip.
There are two strong indications that the
barrier to ROL is of adaptive significance to
plants under waterlogged conditions: (i)
adapted species appear to be able to induce
the barrier when exposed to waterlogged or
hypoxic conditions; and (ii) tight barriers
tend to occur in wetland but not dryland
species. Colmer et al. (1998) examined the
effects on ROL in the roots of four rice
98 D.J. Mullan and E.G. Barrett-Lennard

(a) (b)

40 40

Porosity (% root volume)

30 30

20 20

10 10

0 0
H1 H2 H3 H4 H5 H1 H2 H3 H4 H5
Habitat Habitat
Fig. 6.2. Effects of habitat of origin on the root porosity (95% confidence interval) of plants grown under:
(a) drained, or (b) waterlogged conditions (water level 10–20 mm above soil surface) for ~1 month
(calculated from data of Justin and Armstrong, 1987). The plants were from the following habitats: H1 –
standing water above the soil surface for all or most of the year (21 species); H2 – wet soils which are
saturated with water for most of the year (59 species); H3 – damp soils which may be occasionally wet
(52 species); H4 – ‘normal’ moist soils, such as a typical field soil (38 species); and H5 – dry soils which
crumble to the touch and are usually found on high ground or above very porous rock (16 species). Plant
species generally occurred across more than one habitat; we have only used species where porosity
data were available for both drained and flooded conditions.

varieties exposed to aerated or stagnant
nutrient solutions. The ratio of ROL at 5 mm
from the root tip to ROL at 35 mm from the
root tip varied from ~0.3 to 1.0 when the
plants were grown in well-aerated nutrient
solutions, indicating that under these condi­
tions the plants had a weak or partial barrier
to ROL. However, with three of the rice
varieties, this ratio increased to values
greater than 20 when the plants were grown
in stagnant nutrient solutions, showing that
hypoxia had induced a tight barrier to ROL
(Colmer et al., 1998).
McDonald et al. (2002) examined the
presence of barriers to ROL in ten species
from the Poaceae and two species from the
Cyperaceae representing plants from a range
of wetland and dryland habitats. Using the
definition above, ‘tight’ barriers to ROL
occurred in eight out of nine wetland species
grown under stagnant conditions; the single
exception was in the pasture species Phalaris
aquatica, which only had a ‘partial’ barrier to
ROL. In contrast, with the three dryland
species, the barriers to ROL were ‘partial’ or
‘weak’ (McDonald et al., 2002).
Inundation
Many saltland habitats are also subject to
inundation, but the impacts of this combi­
nation of stresses on the growth and survival
of crop plants are poorly understood. Within
cereal crops, nearly all inundation research
has focused on rice under non-saline condi­
tions (e.g. Setter et al., 1987, 1988). Our
understanding of the kinds of physiological
adaptations that are important to inunda­
tion come largely from studies of rice and
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 99

(a) 0.4

0.3
Adventitious
root DM 0.2
Shoot DM
0.1 P = 0.013
0
0 10 20 30

(b) 400
300
Longest
adventitious 200
root (mm) 100
P = 0.005
0
0 10 20 30
Adventitious root porosity
(% volume)
Fig. 6.3.  Relationship between the porosity of adventitious roots and: (a) ratio of adventitious root dry
mass (DM) to shoot DM; and (b) length of the longest adventitious root. Data are for ten genotypes from
the Triticeae grown in stagnant nutrient solutions for 70 days (McDonald et al., 2001).

plants that occur naturally on saline and
non-saline marshland (e.g. Voesenek et al.,
2004; Pedersen et al., 2006; Rich et al., 2008;
Colmer et al., 2009).
Inundation damages plant growth mostly
because the column of inundating water
limits gas (mainly O2) exchange between
leaves and the atmosphere (Colmer, 2003).
Oxygen concentrations in inundating water
are generally highest near the water surface,
decrease with depth, and fluctuate diurnally,
increasing in the day and decreasing at night
(Setter et al., 1987). In addition, there can be
an attenuation of light by the column of water
and material suspended in it. For example, in
partially inundated rice fields in Thailand,
only 20–52% of ambient light reached the
water surface due to shading by leaves, and
this was attenuated a further 15–20% by 0.2
m of water (Setter et al., 1987). Further to
this, areas that are inundated are also likely to
have waterlogged soils after the inundation
has receded, so the mechanisms described
above for waterlogged soils are also relevant
to the inundated situation.
According to Voesenek et al. (2004), the
key physiological traits associated with inun­
dation tolerance in plants centre around
factors that enable plants to:
• Avoid inundation through being present
as dormant seeds or quiescent perennat­
ing organs.
• Ameliorate inundation through the fast
elongation of leaves that can act as ‘snor­
kels’ with the atmosphere, the develop­
ment of longitudinally connected
gas-filled channels and barriers to ROL to
facilitate inter-organ gas diffusion, and
the continuation of photosynthesis under
water to generate O2 and carbohydrates.
• Tolerate inundation through the genera­
tion of energy without O2 via glycolytic
fermentation and through the reduction
in plant metabolic rates.
It is presently difficult to choose between
these options for crops as little is known
about the selectable variation that exists for
these traits. Rice, arguably the world’s most
inundation tolerant cereal, is known to
employ both tolerance and amelioration
strategies. During germination the seeds use
the energy from fermentation (Setter and
Ella, 1994) to rapidly send a coleoptile to the
100 D.J. Mullan and E.G. Barrett-Lennard
water surface, which acts as a ‘snorkel’ deliv­
ering O2 to the seed (Kordan, 1974). Later
the plants develop leaves that elongate suffi­
ciently rapidly to be partly above water
(Kende et al., 1998), and the leaves develop a
non-wetting surface covered with a gas film
that conveys O2 to the roots and CO2 to the
leaves (Pedersen et al., 2009).
Breeding for Tolerance
The improvement of crop performance in
saline, waterlogged and inundated environ­
ments through conventional breeding
programmes has been a challenging pursuit.
While significant increases in crop yields
were achieved in drought and hot environ­
ments during the post-Green Revolution era
(Lantican et al., 2003) large areas of land
subject to salinity, waterlogging and inunda­
tion are still to benefit from such a powerful
and sustained research thrust. Genetic
progress in breeding for tolerance to these
stresses has been slow, as the physiological
components of plant response are complex
and the genetic basis for these responses is
largely unknown (Flowers, 2004). Further­
more, the complexity of the environment
and response of plants to subtle differences
in environmental conditions, such as the
timing, duration and intensity of stress
(Munns, 2002; Setter and Waters, 2003),
confound the identification of beneficial loci.
In spite of the challenges, there remain good
prospects for improvements in crop produc­
tion on salt-, waterlogging- and inundation-
prone soils through improvements in land
management (Adcock et al., 2007; Bhutta
and Smedema, 2007; Singh, 2009; Hobbs
and Govaerts, Chapter 10, this volume) and
plant breeding. Flowers and Yeo (1995) list
three possible solutions to the development
of crops for saline/waterlogged soils: (i) seek
improvement within existing crop genomes;
(ii) incorporate genetic information from
halophytes into crop species; and (iii) domes­
ticate halophytes (Fig. 6.4). These approaches
may help to genetically improve the toler­
ance of crops for salinity, waterlogging and
inundation.
Variation within existing germplasm pools
Genetic variation within cultivated crops
has been identified, but it is unclear if there
exists sufficient diversity to deliver the range
in adapted phenotypes required for adequate
yield gains. It is difficult to accurately deter­
mine the level of diversity within crops due
to differences in genotypes selected for stud­
ies and the contrasting experimental and
environmental conditions in which they are
screened (see the ‘Stresses and the Key Plant
Physiological Adaptations’ section). Perhaps
an appropriate measure of the diversity
within elite material can be performed by
the identification of germplasm registra­
tions and variety releases. For the most part,
there have been few examples of successful
varietal releases targeting either salinity,
waterlogging or inundation tolerance. For
salinity, Flowers and Yeo (1995) report that
from when records began until 1993 they
were only able to identify 25 cultivars from
12 plant species that had been released for
their improved salt tolerance. Flowers (2004)
also reported that between 1993 and 2000
there had been only three additional regis­
trations, including one for lucerne (Al-Doss
and Smith, 1998) and two for rice (Oliver-
Inciong, 1996). Encouragingly, during recent
years the release of varieties with improved
salt tolerance has become more frequent
through using key germplasm sources, such
as ‘Kharchia 65’ in wheat (Rana, 1986), and
‘Pokkali’ and ‘Nona Bokra’ in rice (Gregorio
et al., 2002).
The progress in waterlogging and inunda­
tion tolerance appears to be similar to salin­
ity tolerance. Setter and Waters (2003)
reviewed the genetic diversity for waterlog­
ging tolerance in a collection of wheat, barley
and oat varieties, but little is known of the
diversity available for tolerance to inunda­
tion for these crop species. However, in rice,
crop diversity for submergence tolerance has
been reported (Bailey-Serres and Voesenek,
2008) and the number of tolerant varieties
has increased during recent years, although
adoption by farmers has been limited due to
poor grain yield and quality (Sarkar et al.,
2006). While there seems to be genetic vari­
ation in the primary gene pool of some crop
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 101

Fig. 6.4.  Generalized breeding scheme showing the assessment and incorporation of new genetic
variation for salinity, waterlogging and inundation tolerance. Conventional breeding approaches (1) may
be successful if sufficient genetic variation exists within germplasm (e.g. lucerne, Al-Doss and Smith,
1998; rice, Gregorio et al., 2002; wheat, Setter and Waters, 2003; Munns et al., 2006). When there is
insufficient genetic variation, new diversity can be introduced through domestication (2) (e.g. Distichlis
spp., Yensen and Bedell, 1993), recombinant line introgression (3) (e.g. wheat, Wang et al., 2003),
amphiploid production (4) (e.g. wheat, King et al., 1997), use of transgenics (5) (e.g. wheat, Xue et al.,
2004), use of landraces (6) (e.g. maize, Day, 1987; wheat, Munns et al., 2000; Singh and Chatrath, 2001)
and use of synthetic hexaploids (7) (e.g. wheat, Villareal et al., 2001; Reynolds et al., 2005). Physiological
trait selection and screening (8) (e.g. rice, Gregorio et al., 2002) and marker assisted selection (9) (e.g.
rice, Xu and Mackill, 1996; wheat, Lindsay et al., 2004) may also increase the efficiency of conventional
breeding approaches and contribute to more rapid production of improved populations and cultivars.

species, the low number of currently released
cultivars with tolerance indicates that using
the available germplasm is not likely to be
sufficient and that alternate sources of
genetic variation need to be identified and
utilized.
Introduction of new genetic diversity –
amphiploids and alien introgression lines
The introduction of new genetic diversity
into the gene pools of crop species, which
have undergone a narrowing of their genetic
base during domestication, is essential for
crop improvement. Crop wild relatives have
provided plant breeders with potentially
useful genetic resources for tolerance to
abiotic stress for over a century (Prescott-
Allen and Prescott-Allen, 1986). As plant
breeders have demanded more diversity in
germplasm the progenitors of crops and
closely related species have been increas­
ingly utilized. Trends since the mid-1980s
show an increased use of wild species, with
over 100 traits being transferred to crop
102 D.J. Mullan and E.G. Barrett-Lennard
species during the last 20 years (Hajjar and
Hodgkin, 2007). Additionally, while pest and
disease resistance is the predominant target
of wild introgressions, due to being control­
led by fewer genes and easier screening
within breeding programmes, the incorpor­
ation of abiotic stress tolerance is increasing
(Hajjar and Hodgkin, 2007). However, only a
handful of examples of wild relatives contrib­
uting genetic resistance to abiotic stresses in
crops have reached the stage of cultivar
release, even though many wild relatives
with potential have been described (Hajjar
and Hodgkin, 2007; Colmer and Flowers,
2008; Flowers and Colmer, 2008).
Despite the low number of released culti­
vars for salt, waterlogging and inundation
tolerance, there exists a large resource of
potential germplasm for increasing the
genetic base of crop plants. For example, salt
tolerance during late vegetative stages has
been reported among wild species of tomato
(Lycopersicon pennelli and Lycopersicon peru-
vianum) (Tal and Shannon, 1983). Colmer et
al. (2006) also list 38 species as possible
sources of salt tolerance in the Triticeae, with
examples from the Triticum, Aegilops,
Elytrigia, Elymus, Thinopyrum, Leymus and
Hordeum species. Further to this, when
Munns et al. (2000) screened 54 Triticum
turgidum tetraploids comprising the subspe­
cies durum, turgidum, polonicum, turanicum
and carthlicum, they identified large and
useful genetic variation for improving the
salt tolerance of durum wheat. From this
study, Line 149, derived from a cross between
a Triticum monococcum (accession C68-101)
and a durum cultivar, ‘Marrocos’ (The, 1973),
was selected with a very low Na+ uptake.
Genetic studies of the low Na+ phenotype
led to the mapping of two quantitative trait
loci (QTLs), designated Nax1 and Nax2.
Molecular markers closely linked to the loci
are being used to select low Na+ progeny in a
durum and bread wheat breeding programme
(Lindsay et al., 2004; Byrt et al., 2007).
Another notable example of the successful
introduction of new genetic diversity is the
use of the highly salt tolerant landrace
‘Kharchia’. Salt tolerance from ‘Kharchia 65’
was hybridized with a high-yielding wheat
variety (‘WL 71 I’) to develop India’s first
systematically bred salt-tolerant wheat culti­
var (‘KRL I-4’) at the Central Soil Salinity
Research Institute, Karnal (Singh and
Chatrath, 2001). Likewise, the tolerance of
rice to submergence is improved through
the introgression of the Sub1 locus. The Sub1
locus is derived from the landrace ‘FR13A’,
and accounts for 70% of the phenotypic vari­
ation in submergence tolerance (Xu and
Mackill, 1996). Through marker assisted
selection (MAS), the Sub1 locus has been
introgressed into mega-varieties and is
currently undergoing advanced stages of
field evaluation. The new varieties promise
to be more widely adopted by farmers due to
improved yield and quality characteristics.
The development of amphiploids and
alien introgression lines is one approach
that has been used to generate additional
genetic variation in crop species, but great
care must be taken in the choice of parents
in the development of such hybrids. Reading
the literature we sense that the develop­
ment and testing of amphiploids so far has
largely been opportunistic rather than stra­
tegic. However, the work of Professor Tim
Colmer and his colleagues stands as an
exception in this area. This group identified
Hordeum marinum as a source of genes for
salt and waterlogging tolerance that could
be transferred into bread wheat (Colmer et
al., 2005). Systematic assessments were
made of a range of accessions of H. marinum
for tolerance to salinity (Garthwaite et al.,
2005), waterlogging (Garthwaite et al.,
2003, 2008) and the interaction between
these two stresses (Malik et al., 2009), and
some of these lines have now been incorp­
orated into amphiploids with wheat (Islam
et al., 2007).
However, perhaps even this work could
develop further. We suggest that it may not
be enough simply to create amphiploids
using the natural variation within species.
Perhaps the creation of better adapted
amphiploids should be preceded by the
breeding of better wild grass partners as a
preliminary step. The case for this can be
argued using the data of Malik et al. (2009).
These workers assessed the impacts of the
imposition of 200 mM NaCl with or without
hypoxia on the growth and ion relations
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 103

of eight accessions of H. marinum subsp. (a)

0
gussoneanum and nine accessions of H. mari-
num subsp. marinum. H522 H823 H826
In all accessions, increasing the salinity in

Decrease in RGR (% of control)

–10
the nutrient solution from 0 to 200 mM
NaCl increased the concentration of Na+ in
the youngest fully expanded leaf and –20
decreased relative growth rate (RGR) of the
shoot, but there was no correlation between
these two characters (Fig. 6.5a). However, –30
some of the individual accessions were of
interest. Salinity caused only slight decreases
in the RGR of three accessions (H522, H823 –40
and H826; decreases of 14–15% of controls), H87
and two of these (H522 and H826) had quite
large differences in the change in Na+ concen­ –50
tration in the youngest fully expanded leaf 0.0 0.2 0.4 0.6 0.8
associated with salinity. Clearly, all three +
Change in Na (mmol/g DM)
accessions have traits of interest with respect
to salinity tolerance, but H826 also has a
considerable ability to tolerate Na+ in the
leaves. The imposition of hypoxia in addition (b)
to salinity (Fig. 6.5b) caused an additional 0
Additional change in RGR (% of control)

decrease in shoot RGR (compared to aerated H87

non-saline controls) and this was generally
associated with further change in the –10
concentration of Na+ due to hypoxia. With H823
this combination of stresses accession H87
was of interest; with the imposition of
hypoxia the Na+ concentration in the –20
younges­t leaf of this plant actually decreased
and this plant had only a slight (7%) further
decrease in RGR. Data published by the –30 H826
authors showed that H87 had a very tight
barrier to ROL that was induced by the H522
combination of salinity and hypoxia (Malik
et al., 2009). –40
What this analysis shows is that none of –0.4 –0.2 0.0 0.2 0.4
the accessions appears to have the combined +
Change in Na (mmol/g DM)
traits for tolerance to salinity and hypoxia
that we might require in the ideal parent for Fig. 6.5.  Effects of salinity and hypoxia on the
an amphiploid; accession H87 had poor relative growth rate (RGR) and Na+ relations in the
prospects under saline aerated conditions youngest fully expanded leaf of accessions of
and accessions H522 and H826 (particu­ Hordeum marinum (data from Malik et al., 2009).
larly) had poor prospects with the imposi­ (a) Relationship between decrease in RGR and
change in Na+ due to the imposition of salinity
tion of hypoxia under saline conditions (Fig.
under aerated conditions. (b) Relationship between
6.5b). Clearly, a crossing programme that the further decrease in RGR and the further
co-locates genes associated with strong salt change in Na+ due to the imposition of hypoxia to
tolerance (accessions H522, H823 and H826) plants under saline conditions. Open symbols =
with genes associated with strong tolerance subsp. marinum; closed symbols = subsp.
to hypoxia (H87) might yield a better parent gussoneanum. H-numbers are accessions referred
for incorporation into an amphiploid. to in the text. DM, dry mass.
104 D.J. Mullan and E.G. Barrett-Lennard
Alternatively, H823 would appear to be a
reasonable compromise as a candidate wild
grass parent.
There are significant limitations to the
successful introgression of favourable genes
from wild species, including plant responses
to complex interactions between saline,
waterlogged and inundated environments,
difficulties with interspecific crossability and
the retention of undesirable agronomic traits.
The importance of crop adaptation to
combined salinity and waterlogging stress
(Barrett-Lennard, 2003) emphasizes the need
for crop adaptation to both stresses, as culti­
vars bred for only one abiotic constraint may
have limited success in farmers’ fields. Since
the late 1980s there have been major advances
in hybridization methodologies, molecular
technologies and breeding strategies. This
has reduced the limitations associated with
interspecific crossability, and has enabled
more efficient alien introgression with
reduced undesirable ‘linkage drag’. Techno­
logi­cal advances, combined with a greater
understanding of the complex physiological
mechanisms underlying salt, waterlogging
and inundation tolerance, have enabled an
increased incorporation of distantly related
taxa and will continue to provide vital genetic
diversity for improvements in crop yields in
hostile environments.
Domestication of halophytes
Dryland soils that have ECe values greater
than ~8 dS/m can be described as being
highly salt affected and such soils are gener­
ally too saline for major crops to produce
commercial yields. The growth of plants for
commercial use in these landscapes necessi­
tates the use of halophytes. The case for this
is made more compelling by the fact that
many halophytes have an increase in growth
with some salinity (50–200 mM NaCl) in the
root zone (Greenway and Munns, 1980).
Current databases list more than 1800 halo­
phytes that have potential uses for man
(USDA, 2009). However, in practice few of
these plants have had widespread commer­
cial adoption. One exception has been the
use of saltbushes (Atriplex species) in
Australia to provide fodder for sheep (Barrett-
Lennard et al., 2003). Although these plants
will withstand salt concentrations of more
than seawater salinity in the root zone
(Aslam et al., 1986), their optimal growth in
the field occurs more in the ‘moderately
saline’ to ‘highly saline’ range (ECe values
4–16 dS/m; E.G. Barrett-Lennard and M.
Altman, unpublished results, 2008). Recent
surveys suggest that more than 245,000 ha
of salinized agricultural land are now
managed in farming systems based around
the use of these plants (Trewin, 2002).
From the point of view of cropping, we
cannot ignore the pioneering work of the
late Dr Nicholas Yensen, who made a number
of selections within the halophytic genus
Distichlis to produce accessions suited to the
production of grain, forage and turf (Yensen
and Bedell, 1993). In an assessment of six
lines of Distichlis grown for 18 weeks over
the North American summer, three lines
had growth optima at ~90 mM NaCl, but
two of the lines assessed had growth optima
at ~290 mM NaCl (Yensen et al., 1985).
Despite the promise of this work, Yensen’s
Distichlis lines are still only planted on a rela­
tively limited scale.
Breeding approaches
Breeding approaches for improving abiotic
stress tolerance in crop species are evolving at
a rapid pace. With the development of molec­
ular technologies, transgenic approaches have
become a prominent part of many research
initiatives. Genetic transformation currently
assists in the study of cellular mechanisms
underlying salt, waterlogging and inundation
tolerance, and there have been many poten­
tially beneficial genes identified for genetic
transformation (Dennis et al., 2000;
Yamaguchi and Blumwald, 2005; Munns,
2005; Agarwal and Grover, 2006; Munns and
Tester, 2008; Flowers and Colmer, 2008).
Table 6.2 details a range of candidate genes
for salinity, waterlogging and inundation and
their expected function in crop plants.
However, in spite of the increasing volume of
knowledge on candidate genes and their func­
tion in plants, the future role of transgenically­
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 105

Table 6.2. Selected genes associated with salinity, waterlogging and inundation.
Candidate
Stress gene Protein family Role in plant function
Salinity NHX Vacuolar Na+/H+ The NHX antiporters (NHX1:5) transport Na+ across
antiporter the tonoplast and into vacuoles and are driven by
an electrochemical gradient of protons. The over­
expression of AtNHX1 in transgenic Arabidopsis
has been shown to improve salt tolerance; plant
growth and development were unaffected at up to
200 mM NaCl. Field trials have also shown benefits
of the transgenic expression of NHX in wheat
through improvements in yield under salt stress
(Munns, 2005; Flowers and Colmer, 2008; Munns
and Tester, 2008).
SOS Plasma membrane The SOS1 transporter is important for the extrusion
Na+/H+ antiporter of Na+ from plant cells. It is responsible for the
exchange of Na+ and H+ ions across the plasma
membrane (Na+ outwards). The activation of this
transporter is regulated by the SOS2 and SOS3
genes, allowing the cell to respond to different
cellular conditions. The genes have the potential to
enable the efflux of Na+ from roots, however, the
exact role of SOS1 in salinity tolerance remains
uncertain (Munns, 2005; Flowers and Colmer,
2008; Munns and Tester, 2008).
HKT High-affinity K+ HKT1 was originally isolated from wheat roots by
transporter expression cloning, and at low external Na+
concentrations plays a role in K+ uptake from soil
and nutrient transfer of K+ into leaves. However, the
activity of HKT1 is also known to facilitate Na+
influx into tissues in high Na+ environments.
Functional analysis in Arabidopsis suggests that
the gene may also be involved in Na+ recirculation
from shoots to roots and maintenance of shoot K+
homoeostasis (Munns, 2005; Flowers and Colmer,
2008; Munns and Tester, 2008).
LCT1 Low-affinity cation Studies with yeast cells indicate that the LCT1
transporter transporter is located on the plasma membrane
and is responsible for the transport of Na+, K+,
Ca2+ and Cd2+. While the exact physiological role of
LCT1 has not yet been established, it is known that
LCT1 is an important contributor to Na+ influx in
wheat at high external Na+ concentrations and
preliminary investigations indicate that modification
of the selectivity of LCT1 has the potential for
improving salt tolerance in plants (Flowers and
Colmer, 2008).
AVP1 Vacuolar AVP1 has the ability to increase the vacuole
H+-pyrophosphatase transmembrane proton gradient, increasing the
(PPiase) capacity for sequestration of cations in the vacuole,
and thus reducing the toxic effects of Na+ in the
cytosol. PPiase proton pumps appear to be
important for enhancing salt tolerance as they
generate the primary driving force for Na+ transport
via proteins such as SOS1 and NHX1 (Munns,
2005; Munns and Tester, 2008).
Continued
106 D.J. Mullan and E.G. Barrett-Lennard

Table 6.2. Continued

Candidate
Stress gene Protein family Role in plant function
Waterlogging PDC Pyruvate PDC (2-oxo-acid carboxylase) is the first enzyme
and decarboxylase (PDC) channelling carbohydrates towards alcoholic
inundation (alcohol fermentation) fermentation and is considered to be the rate-
limiting step in this pathway. A number of different
plant PDC genes have been cloned and
sequenced. Maize and rice are the most
extensively analysed plant systems for the
characterization of PDC enzymes and their
corresponding genes. It has been hypothesized
that change in the subunit composition confers
upon rice seedlings the capacity to carry out active
ethanol fermentation during prolonged treatment
with anoxia (Dennis et al., 2000; Agarwal and
Grover, 2006).
ADH Alcohol ADH leads to the conversion of acetaldehyde to
dehydrogenase (ADH) ethanol in the final step of the alcoholic
(alcohol fermentation) fermentation pathway. The increased expression of
ADH genes in response to O2 deprivation has been
identified and studied in many crop species,
including barley, rice, maize, cotton and tomato
(Dennis et al., 2000; Agarwal and Grover, 2006).
SuSy Sucrose synthase Increased SuSy activity after the onset of hypoxia
(SuSy) (carbohydrate has been documented in many crop species
metabolism) including wheat, maize, rice and potato. SuSy
exists in the cytoplasm of many non-photosynthetic
tissues, where it increases sucrose cleavage,
providing carbohydrates for alcoholic fermentation
and the synthesis of storage and structural
polymers (Dennis et al., 2000; Agarwal and Grover,
2006).
Hb Haemoglobin Haemoglobins are known for their ability to act as O2
carriers to facilitate O2 delivery. At low O2 tensions
they may also act as O2 sensors to regulate gene
expression. Transgenic studies in lucerne and
maize indicate a beneficial role of haemoglobins in
nitric oxide regulation and root growth under low O2
stress (Dennis et al., 2000; Agarwal and Grover,
2006).

engineered salinity, waterlogging or inunda­ or enzymes leading to the synthesis of func­

tion tolerance in crop species is uncertain.
The complexity of plant response and the
environment suggests that single gene modi­
fications may not contribute a significant
improvement in salt, waterlogging or inunda­
tion tolerance. Nevertheless, the process of
genetic modification may contribute some
advantage if the gene is involved in signalling
and regulatory pathways (Seki et al., 2003),
has a pleiotropic effect, or encodes a protein
conferring stress tolerance (Wang et al., 2004)
tional and structural metabolites (Apse and
Blumwald, 2002). In fact, claims of improved
tolerance through genetic modification have
been made, but are difficult to substantiate
due to experimental designs and data sets
that do not represent the target environment
(Flowers, 2004). Meanwhile, there are other
promising breeding approaches that may be
utilized such as targeting physiological traits
within conventional breeding programmes
(Fig. 6.4).
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 107
Blum (1989) and Yeo et al. (1990)
suggested that targeting physiological
parameters would simplify the genetics and
breeding procedures for tolerance to abiotic
stress. The approach has become an import­
ant component of international wheat
breeding initiatives (Reynolds and Pfeiffer,
2000; Reynolds and Trethowan, 2007) and
has also been used as a basis for rice selec­
tions (Dedolph and Hettel, 1997). Key
components of physiological trait breeding
include: (i) design of a model encompassing
physiological traits contributing to tolerance
in a crop species; (ii) identification of vari­
ation for the traits within the physiological
model; and (iii) evaluation of the potential
genetic gains contributed by each of the
components of the model, so that traits may
be combined in such a way as to maximize
additive genetic gains. Flowers and Yeo
(1995) advocate the use of a physiological
trait-based breeding approach and report on
the feasibility of increasing the resistance of
salt-sensitive species; this approach has
been successful in rice (Gregorio et al., 2002).
In the past there have been several chal­
lenges inhibiting the successful implemen­
tation of this approach, including the need
for time-consuming or destructive physio­
logical screens. However, technology is now
better able to overcome some of these limi­
tations through the development and
increased efficiency of MAS (Bonnett et al.,
2005; Kuchel et al., 2005) and high-through-
put phenotypic analysis (Babar et al., 2006;
Ruuska et al., 2006; Olivares-Villegas et al.,
2007).
Conclusions
A number of priorities for research, develop­
ment and agricultural evolution have become
evident in the writing of this chapter.
There needs to be a much better
understanding of the impacts of climate
change
While it is likely that climate change will
impact on salinity, waterlogging and inun­
dation in the future, the spatial extent of
these impacts and the time frames over
which these stresses are likely to develop are
unknown. The current evidence in this area
is largely anecdotal. There is a critical need
for better modelling so that the areas of land
at future risk and the likely impacts of these
effects on human populations can be esti­
mated. Some of the most severely affected
populations will be impoverished subsist­
ence farmers (e.g. in Bangladesh).
There needs to be attitudinal change about
what may be possible in landscapes at risk
In many ways salinity has been a cause of
agricultural decline for thousands of years.
The idea that land threatened by salinity can
be planted to salt-tolerant plants and made
productive is relatively recent (Teakle and
Burville, 1945), but this hope needs to be
promoted realistically and responsibly at the
policy level and to affected communities.
We need a holistic approach to the use of
the land at risk
Any attempt to breed crop plants with toler­
ance to salinity, waterlogging and inunda­
tion needs to be integrated into larger efforts
in the sustainable use of these landscapes.
These will necessarily involve the use of
combinations of crops, pastures with graz­
ing animals and trees. Developing and imple­
menting productive systems around these
elements will require researchers (agrono­
mists, silviculturalists, soil scientists and
agricultural extension specialists) working
in partnership with groups of farmers
(Wassmann et al., 2009).
We need to develop suitable land
engineering and management options
Further advances must be made in the effect­
iveness of current engineering and manage­
ment options to address subsoil constraints.
The options must be evaluated for cost
effectiveness and likelihood of success, with
engineering, management and plant breed­
ing becoming more fully integrated (Adcock
et al., 2007; Bhutta and Smedema, 2007;
Singh, 2009). Conservation agriculture is
108 D.J. Mullan and E.G. Barrett-Lennard
one example where changes in agricultural
practice may have beneficial effects, includ­
ing the amelioration of salinity and sodicity
(Hobbs and Govaerts, Chapter 10, this
volume). Critical to the implementation of
successful engineering and management
options will be the assessment of the impacts
of such activities on the environment and
catchment hydrology.
We need to take advantage of existing plants
with the required tolerances wherever
possible
The fastest way to develop plants for land­
scapes threatened by salinity, waterlogging
and inundation is to introduce plants with
natural tolerance to these conditions from
elsewhere. Naturally, this needs to be done
carefully to avoid the possibility of intro­
duced plants becoming weeds in their new
locations. So far, the development of pasture
systems for saltland has occurred primarily
through the collection and domestication of
existing plants (e.g. Rogers and Bailey, 1963;
Malcolm et al., 1984). More recently, large
databases have been developed of poten­
tially useful halophytes (Aronson, 1989;
USDA, 2009), and some of the more prospec­
tive species have been reviewed for tolerance
to salinity and waterlogging as desktop exer­
cises (Rogers et al., 2005), and assessed
experimentally (Teakle et al., 2006; Rogers
et al., 2008). This kind of activity also needs
to be undertaken for the new areas at risk.
We need much better information about the
impacts of the stresses on yield
Reasonable data are presently available on
the effects of salinity alone on crop yield
(Maas and Grattan, 1999; Steppuhn et al.,
2005); how these impacts are modified by
waterlogging and inundation is largely
unknown.
We need better land capability
assessment tools
The interactions between salinity, waterlog­
ging and inundation almost certainly affect
the zonation of plants in agricultural land­
scapes (Bennett et al., 2009; this chapter).
Farmers need access to simple tools to assist
them to recognize differences in saltland
capability, so that land can be assigned to its
optimal use (cropping, pasture or land with­
held from agricultural use) (Bennett et al.,
2009). In some cases, establishing mixtures
of plants may create greater ecological resil­
ience. Tools are also required to help farmers
identify where in the landscape other
en­gineering and agronomic strategies may
be relevant (e.g. different kinds of drainage,
use of mulches, phytoremediation, fertiliz­
ers, etc.).
We need appropriate crop breeding targets
This chapter has discussed more than 15
traits of potential value in assisting plants to
grow in landscapes affected by salinity,
waterlogging and inundation. The develop­
ment of adapted crops for such landscapes
will therefore presumably require the pres­
ence of even more genes in crop plants than
has hitherto been recognized by commenta­
tors like Flowers and Yeo (1995). How should
we go about this? Several approaches seem
obvious:
• We need good ‘proof of concept’ examples. If
the adaptive value of introducing genes
for salt and waterlogging tolerance can
be shown for one crop plant, other
programmes to improve other species
will follow. The work developing salt- and
waterlogging-tolerant amphiploids from
the wild grass H. marinum and bread
wheat (reviewed in Colmer et al., 2006) is
a good example of such a proof of concept
programme, but even here, a great deal of
further work will be required before this
activity results in the development of a
better adapted cereal.
• We should focus on crops that already have
traits of interest. Some crop plants already
have some of the required relevant traits;
under these conditions, all plant breeders
need to do is add traits that are missing.
For example, rice has exceptional toler­
ance to waterlogging and inundation, but
an improvement in the salt tolerance of
this plant would be a great asset. Work to
 Breeding for Tolerance to Salinity, Waterlogging and Inundation 109
improve the salt tolerance of this species
has therefore been most timely (Flowers
and Yeo, 1981; Yeo et al., 1988; Khatun
and Flowers, 1995). Further to this, there
are some barley cultivars that presently
have good salt tolerance (Ayers et al.,
1952); efforts could be made to introduce
genes for waterlogging tolerance into this
material.
• We should continue to develop crop plants
with high vigour. Richards (1995) makes
the reasonable case that in any landscape
with spatially variable salinity, the great­
est amount of production will always
occur on the least saline land. He advo­
cates the development of crop plants that
give improved growth under the least
affected conditions as an important strat­
egy in maximizing yields overall.
• We should continue to study the physio-
logical mechanisms associated with plant
adaptation in naturally saline/waterlogged
environments. One intriguing genus
worthy of further study is Puccinellia. Of
all terrestrial plants studied, Puccinellia
spp. appear to be the major exception to
the general principle that waterlogging
under saline conditions increases the
uptake of salt ions to the shoots. On the
contrary, with Puccinellia peisonis and
Puccinellia ciliata, waterlogging under
saline conditions decreases rates of salt
uptake to the shoots, which increases
plant growth (Stelzer and Läuchli, 1977;
Jenkins et al., 2010). The mechanisms
that the plants use to achieve this feat are
only partly understood.
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 7
Multi-location Testing as a Tool to
Identify Plant Response to Global
Climate Change

Hans-Joachim Braun, Gary Atlin and Thomas Payne

Abstract
Plant breeding, using the combined potential of conventional, molecular and genetically modified
technologies, will provide cultivars with greatly enhanced nutrient and water-use efficiency, enhanced
tolerance to heat and drought, resistance to diseases and appropriate end-use and nutritional quality,
and, possibly most important, increased ability to cope with the increasing extremes in temperature
and precipitation occurring at one location over years. Modern crop cultivars developed by seed
companies, international crop research centres and national breeding programmes often exhibit very
wide geographical adaptation, as well as broad adaptation to the range of environmental and
management conditions that occur within and between a target population of environments, or mega-
environments. To identify such cultivars, multi-location testing done by the International Maize and
Wheat Improvement Center (CIMMYT) and the International Rice Research Institute (IRRI) remains
the most efficient system. International evaluation networks based on exchange of and free access to
germplasm and multi-location testing are therefore a cornerstone in the strategies and efforts to
develop wheat, rice and maize germplasm that is adapted to the increasingly variable growing
conditions encountered due to global climate change. Information from such trials must be combined
with information from managed stress trials. Wide performance adaptation is essential to respond to
global climate change, to the vagaries of spatial heterogeneity within farmers’ fields and their
production input management efficacies, and from unpredictable temporal climatic seasonal
variability.

Introduction greatest for the production of the staple

One-sixth of the world’s human population
has insufficient food to sustain life, and food
supply will need to double by 2050 to meet
this demand. Agricultural genetics is one of
the components of the solution to meet this
challenge (Nature Genetics, 2009). The most
serious challenges economies and societies
will face over the next decades include
providing food and the water needed for
food production, to a world that will see its
population increase by a third in the face of
mounting environmental stresses, worsened
by the consequences of global climate
change.
The challenge of increasing food produc-
tion in the face of climate change will be
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 115
grain crops that form the basis of diets the
world over. Wheat, maize and rice are the
three major staples, covering together 40%
of the global crop land of 1.4 billion ha
(FAOSTAT, 2009). Together they provide
37% of all protein, and 44% of all calories for
human consumption (Table 7.1). Each crop
provides more than 50% of the daily caloric
uptake in regions with high consumption,
for example North Africa and Central Asia
for wheat, sub-Saharan African countries
and mesoamerican countries for maize, and
South and Eastern Asian countries for rice,
and especially among the poorest people in
these regions. Wheat is, with 220 million ha,
the most widely grown crop followed by
maize with 158 million ha and rice with 155
116 H.-J. Braun et al.
Table 7.1.  Percentage of calories and protein in the human diet obtained from wheat, maize and rice
globally and in the developing world (FAOSTAT, 2009).
Grain crop Region
Maize World
Developing countries
Wheat World
Developing countries
Rice World
Developing countries
Total from wheat, World
rice and maize Developing countries
million ha. Average yield of maize, rice and
wheat is 5, 3.9 and 3 t/ha, respectively.
Although around 135 countries produce
more than 10,000 t of maize compared with
100 countries that produce more than
10,000 t of wheat, wheat shows the widest
geographical distribution because it is grown
from Ecuador to 67°N in Scandinavia to 45°S
in Argentina, Chile and New Zealand
(Trethowan et al., 2005). Maize is grown
from 55°N in Western Europe to 45°S in New
Zealand. Rice is grown in a narrower
geographic belt between 40°N in Japan and
30°S in Brazil, but is grown over a very wide
range of hydrological environments within
this area.
Plant breeding, using the combined
potential of conventional, molecular and
genetically modified technologies, will
provide cultivars with greatly enhanced
nutrient and water-use efficiency, enhanced
tolerance to heat and drought, resistance to
diseases and appropriate end-use and nutri-
tional quality and, possibly most important,
increased ability to cope with the increasing
extremes in temperature and precipitation
across regions and over years. The wide range
of environments in which wheat, rice and
maize are now grown indicates that the
genetic variability exists within these species
to cope with the large and rapid climate
shifts we are facing, but more integrated and
collaborative approaches to crop variety
evaluation and the exchange of seed and
information will be required to avoid rapid
declines in production in severely affected
regions. In this chapter, we intend to survey
the methods by which breeding programmes
Calories (%) Protein (%)
5 4
6 5
19 20
17 19
20 13
25 18
44 37
48 42
cope with environmental variability, and
consider how these methods may be applied
to the problem of coping with rapid climate
change in crop production systems. The
chapter describes how multi-location test-
ing, as well as managed stress screening and
improved information flow to national and
regional breeding programmes, can help
buffer important crop production systems
against the disruptions likely to arise from
global climate change. The emphasis will be
on wheat, with supporting information from
maize and rice. Other chapters in this book
address specific aspects of genetic improve-
ment, including breeding for disease resist-
ance (Legrève and Duveiller, Chapter 4),
adaptation to heat and drought stress
(Reynolds et al., Chapter 5), adaptation to
salinity, waterlogging and inundation
(Mullan and Barrett-Lennard, Chapter 6),
and genetic approaches to reduce green-
house gas emissions associated with crop
production (Parry and Hawkesford, Chapter
8).
International Cooperation
International and regional cooperative agri-
cultural research has historically been an
example, par excellence, of the open source
approach to biological research. Beginning
in the 1950s, and especially in the 1960s, a
looming global food crisis led to the develop-
ment of a group of international agricultural
research centres with a specific mandate to
foster international exchange and crop
improvement relevant to many countries.
 Multi-location Testing to Identify Plant Response 117
This formalization of global biological
commons in genetic resources was imple-
mented through an elaborate system of
international nurseries with a breeding hub,
free sharing of germplasm, collaboration in
information collection, the development of
human resources, and an international
collaborative network (Lantican et al., 2005;
Reynolds and Borlaug, 2006; Dixon et al.,
2007). The international crop improvement
networks implemented by the International
Maize and Wheat Improvement Center
(CIMMYT) and the International Rice
Research Institute (IRRI), and evaluation
networks prevalent throughout the USA,
Canada and Australia operate an open source
system in practice and have impacts on
world poverty and hunger. The open source
approach is just as relevant today, as
witnessed by current crises in food prices
and looming crop disease problems of global
significance (Byerlee and Dubin, 2008).
Multi-environment trials and managed
stress screens: tools for assessing crop
adaptation
Modern crop cultivars developed by seed
companies, international crop research
centres and large national breeding
programmes often exhibit very wide
geographical adaptation, as well as broad
adaptation to the range of environmental
and management conditions that occur
within a target population of environments
(TPE). For example the popular rice varieties
‘Swarna’ and IR64 are each grown on many
millions of hectares in several Asian coun-
tries, and the maize inbred line CML312 has
contributed to hybrids throughout the Latin
American and African subtropics. For wheat,
megavarieties have existed since wheat
breeding started. Kharkov and Kubanka
occupied one-third of the USA wheat area
after introduction in early 1900. Cultivars
that spearheaded the Green Revolution such
as ‘Siete Cerros’ (also named ‘Mexipak’ and
‘Kalyansona’) were grown on millions of
hectares from North Africa to South Asia.
Selections from the CIMMYT cross ‘Veery’
were released in more than 40 countries
(Skovmand et al., 1997). The Russian winter
wheat Bezostaya dominated in Eastern
Europe and West Asia. This breadth of adap-
tation has been achieved in different ways by
different breeding programmes, but the
most important tool has been the extensive
field testing of experimental breeding lines
in many environments during the selection
process. Increases in tolerance to a range of
stresses such as drought, low fertility and
cold in US Corn Belt maize, for example,
have contributed greatly to yield gains
(Castleberry et al., 1984; Duvick, 1997;
Tollenaar et al., 2000) but have not resulted
from direct selection for any of these
stresses. Rather, they have resulted mainly
from the broad-scale multi-location hybrid
testing programmes of commercial maize
breeding companies that effectively sample
conditions occurring in farmers’ fields.
Modern commercial breeding pro­­
grammes, and a few public-sector
programmes, evaluate new cultivars in trials
sampling their TPE over hundreds of loca-
tions and several years. With such extensive
testing, the odds are good that some sites
will be affected by drought, flooding and
heat, and can be used to characterize culti-
vars for these stresses. However, multi-
envir­onment trials (METs) are also expensive
and complex to conduct, and have been
implemented on a scale that could provide
predictive information for cultivar adapta-
tion to climate change in only a few public
and commercial breeding programmes.
Small breeding programmes serving local
markets often have no access to METs,
sampling a wide range of related envir­
onments outside their jurisdiction, some of
which may not be immediately relevant but
may be useful in predicting responses to
climate change. Better access to information
on cultivar performance in broad-scale
multi-location METs could help local and
regional breeding programmes speed up
their adaptation to climate change.
METs, however, are not the only selec-
tion tools that have been used to achieve
tolerance to a broad range of stresses. Shuttle
breeding in the CIMMYT wheat breeding
programme (Trethowan et al., 2007), selec-
tion in both the wet and the dry seasons in
118 H.-J. Braun et al.
the IRRI irrigated rice breeding programme
(Wassmann et al., 2009a), and managed
drought screening in maize, wheat and rice
have all contributed to the development of
more stress-tolerant cultivars (Bänziger et
al., 2006). All of these techniques, and more
extensive sharing of information and well-
characterized germplasm, are key tools that
will be needed to allow rapid adaptation to a
changing climate.
Compared to maize and rice, the wider
natural adaptation of wheat can be attrib-
uted to the combination of multiple alleles
of photoperiod and chilling (or ‘vernaliza-
tion’) sensitive genes that determine the
crop’s agroecological productivity from high
latitudes to equatorial highlands. Spring
wheats developed by CIMMYT and its
predecessor organizations, that have made
impacts since the Green Revolution, were
photoperiod-insensitive, a prerequisite for
geographic wide adaptation. The breeding
system used to develop such germplasm
consisted of shuttling alternating genera-
tions of wheat between two contrasting
north-to-south environments in Mexico –
the Yaqui Valley (Ciudad Obregon, Sonora)
where days are short during the ‘winter
cycle’ and where photo-insensitivity is
required for earlier flowering to avoid termi-
nal heat stresses, and Toluca (Estado de
Mexico) with longer days and cool nights.
This shuttle was the foundation of the
success of what we know today as the Green
Revolution wheats, whose main output was
a completely new kind of wheat: semi-dwarf,
high yielding, insensitive to photoperiod
and disease resistant (Trethowan et al.,
2007).
The second important component for
success of the shuttle is the multi-environ-
ment testing of lines selected under
the scheme. Every year, several hundred
new wheat lines are sent to around 200
cooperators in more than 50 countries, who
evaluate the material and share the results
with the international wheat community.
Without this International Wheat
Improvement Network (IWIN), in which
basically every major wheat programme
worldwide participates, and which is based
on germplasm and information exchange
between CIMMYT and cooperators (the
International Center for Agriculture in Dry
Areas (ICARDA) uses a similar system) it is
unlikely that wheat developed in Mexico
would have had a global impact on wheat
improvement. Extensive reviews of the
impact from CIMMYT wheat germplasm
have been conducted by Lantican et al.
(2005) and Reynolds and Borlaug (2006).
The information on the performance of the
wheat lines in international nurseries
obtained through IWIN is paramount for
the crossing plan at CIMMYT. Using parents
that performed well across a wide range of
environments allowed increases in the
frequency of desirable alleles in CIMMYT
germplasm and is the basis for the high and
stable yield.
Impact of Climate Change on Wheat
Mega-environments
CIMMYT develops improved wheat germ-
plasm for use in developing and emerging
countries, which grow wheat on about 110
million ha (Lantican et al., 2005). To address
the needs of these diverse wheat growing
areas, CIMMYT uses the concept of mega-
environments (MEs) (Rajaram et al., 1994)
to target germplasm development. A ME is
defined as a broad, not necessarily contigu-
ous, area occurring in more than one coun-
try and frequently transcontinental, defined
by similar biotic and abiotic stresses, crop-
ping system requirements, consumer prefer-
ences, and, for convenience, by a volume of
production. The MEs to which wheat breed-
ing stations participating in IWIN are
assigned are given in Fig. 7.1 (Hodson and
White, 2007a). Germplasm generated for a
given ME is useful throughout it, accommo-
dating major stresses, although it does not
necessarily show good adaptation to all
significant secondary stresses. The defin-
itions for these MEs are based primarily on
moisture regime (irrigated versus rainfed)
and growth habit and, related to this,
temperature (spring versus facultative
versus winter). The wheat area in developing
countries was assigned to twelve MEs, of
which ME1–ME6 are classified as spring
 Wheat Mega-environments

Multi-location Testing to Identify Plant Response
Spring Facultative Winter
ME1 ME7 ME10
ME2 ME8 ME11
ME3 ME9 ME12
ME4
ME5
ME6

Fig. 7.1.  CIMMYT defined wheat production and breeding targeted mega-environments (MEs).

119
120 H.-J. Braun et al.
wheat environments, ME7–ME9 as faculta-
tive and ME10–ME12 as winter wheat envir-
onments. Since every ME corresponds to a
unique combination of these parameters,
each one tends to be associated with a
characteristic set of abiotic and biotic
stresses (Braun et al., 1996).
Hodson and White (2007a) expanded the
criteria to classify wheat MEs by introducing
additional geospatial data and discussed the
impacts of global climate change on wheat
(Hodson and White, 2007b). Table 7.2
summarizes the expected impact of climate
change on the various MEs. The greatest
impact is expected in ME1–ME5, which
include subtropical to tropical spring wheat
regions. An estimated 9 million ha of wheat
in these regions currently experience yield
losses due to heat stresses (Lillemo et al.,
2005). Typically heat-stressed environments
are classified as ME5, with subdivisions for
predominantly humid or dry conditions
(ME5A and ME5B). Wheat regions already
at the limit for heat tolerance, for example in
the Eastern Gangetic Plains of Nepal, India
and Bangladesh, are most likely to suffer and
may see substantial area reductions.
Similarly, under warming, large areas of
ME1 will transition to ME5, as illustrated by
Hodson and White (Chapter 13, this volume,
Fig. 13.3). Positive impacts for ME1,
however, are anticipated from CO2-driven
increases in productivity, accompanied by
increased water-use efficiency.
High elevation, high rainfall environ-
ments (ME2A) will experience reductions in
area as the elevation band providing suitable
temperatures for wheat is displaced upwards.
An agroclimatic study on Ethiopia (White et
al., 2001) concluded that the current wheat
area is largely delimited by high temperature
and that warming would greatly reduce the
area suitable for wheat. If heat tolerance of
currently grown cultivars could be enhanced
by 2°C, the wheat area in the periphery of
the highlands could be nearly doubled. For
the acid soil area in Brazil (ME3) rising
temperatures will further increase the stress
to be similar to ME5. The most severe nega-
tive impact from global climate change is
expected for ME4. Drought and heat are
often associated, and this combination of
warming and water deficits may result in
low-rainfall ME4 areas becoming unsuitable
for wheat production. For temperature
increases up to 2°C this trend may be
partially offset by CO2-driven increases in
productivity and water-use efficiency.
Cool high-latitude spring wheat areas
above 45°N in ME6 of Kazakhstan, Siberia,
China, the USA and Canada may benefit
from the affects of global climate change.
Warmer temperatures should allow earlier
sowing and reduce chances of late-season
frost. Some areas may convert to more
productive winter wheats (ME10–ME12) as
risk of cold-induced winter-kill declines. This
is already happening in Russia, where in
traditional spring wheat areas more winter
than spring wheat is grown today (A.I.
Morgounov, Turkey, 2009, personal commu-
nication). An expansion into areas further
north is also likely (Ortiz et al., 2008). Due
to the low temperatures throughout ME6,
beneficial effects of CO2 on productivity and
water-use efficiency are likely.
Regions where facultative wheat (ME7–
ME9), which is intermediate to spring and
winter wheats, predominates should become
more suitable for autumn- to winter-sown
spring wheats as risk of cold damage
decreases. Some ME7 areas will grow culti-
vars adapted to ME1. The effect on yield
potential in these environments is more
uncertain, but since the growing season will
be shortened, this may open new options for
crop diversification.
Table 7.3 provides estimates for the aver-
age effect of increasing temperatures on
grain yields of wheat, maize and rice. Data
are extracted from Easterling et al. (2007).
In high-latitude regions, yield of all three
cereals will increase, or remain unchanged, if
adaptation measures are taken, such as culti-
var change, change in sowing date and shift
from rainfed to irrigated systems. Without
such measures, yields will decline slightly for
all three crops in the 3–5°C temperature
increase scenario. In low-latitude sites,
where nearly all of the wheat, rice and maize
in developing countries is produced, without
adaptation measures grain yield is estimated
to decrease for all three crops with rising
temperatures. Yield reductions vary from

Table 7.2.  Classification of mega-environments (MEs) used by the CIMMYT Global Maize Program and the CIMMYT Global Wheat Program using qualitative
(ME1–ME12) and geospatial criteria (ME1–ME6).
Latitude Wheat area Temperature Sowing Major biotic and Representative Change in ME due to climate change and conse-
ME (N and S) (million ha) Criteriaa regimeb time abiotic stressesc locations/regions quences for germplasm developmentd
Spring wheat
1 < 40° 32.0 Low rainfall irrigated; Temperate Autumn Lodging, SR, LR, Yaqui Valley, N – Rising temperatures result in large areas evolving
coolest quarter (3 YR, KB, Mexico; to ME5; N – Reduced precipitation in subtropical

Multi-location Testing to Identify Plant Response

consecutive months) Alternaria spp. Indus Valley, regions restricts irrigation; supplementary irrigation
mean minimum Pakistan; results in temporary drought periods requiring
temperature > 3°C, Gangetic germplasm with high yield and tolerance to drought
< 11°C Valley, India; (adapted to ME1 and ME4); P – Reduced irrigation
Nile Valley, due to impact of elevated CO2 on water-use
Egypt efficiency; N – Increased insect problems

2A < 40° 4.0 High rainfall in summer; Temperate Autumn Lodging, sprouting, Highlands East N – Rising temperatures result in some areas evolving
wettest quarter mean SR, LR, YR, KB, Africa and to ME5; N – Reduced precipitation results in areas
minimum temperature Alternaria spp., Mexico, Andes evolving to ME4
> 3°C, < 16°C; wettest Septoria spp.,
quarter (3 consecutive PM, RDC, BYD
wettest months)
precipitation > 250 mm;
elevation > 1400 m

2B < 40° 3.0 High rainfall in winter; Temperate Autumn As for ME2A Mediterranean U – Changes in precipitation patterns in areas will have
coolest quarter mean coast, Caspian variable effects; N – Frequency of climate extremes
minimum temperature Sea over years increase requiring germplasm with high
> 3°C, < 16°C yield potential, wide spectrum of disease resistance
and tolerance to drought

3 < 40° 1.7 High rainfall and acid soil Temperate Autumn As for ME2A + Passo Fundo, N – Rising temperatures result in large areas evolving
(pH < 5.2); climate as acid soils Brazil to ME5; U – Changes in precipitation patterns in
in ME2 areas will have variable effects

Continued

121
Table 7.2. Continued

122
Latitude Wheat area Temperature Sowing Major biotic and Representative Change in ME due to climate change and conse-
ME (N and S) (million ha) Criteriaa regimeb time abiotic stressesc locations/regions quences for germplasm developmentd

4A < 40° 10.0 Low rainfall, winter rainfall Temperate Autumn Drought, Septoria Settat, Morocco; N – Rising temperatures exacerbate water deficits,
dominant; coolest spp., YR, LR, Aleppo, Syria; either further reducing yields or making production
quarter mean minimum SR, RDC, Diyarbakir, uneconomical; P – Reduced water deficits through
temperature > 3°C, hessian fly, Turkey impact of elevated CO2 on water-use efficiency
< 11°C; wettest quarter sawfly, sunnpest
precipitation > 100 mm,
< 400 mm

4B < 40° 5.8 Low rainfall, summer Temperate Autumn Drought, Septoria Marcos Juarez, N – Changes in precipitation patterns likely to increase
rainfall dominant; spp., LR, SR, Argentina drought risk
coolest quarter mean Fusarium spp.
minimum temperature
> 3°C, < 11°C; wettest
quarter precipitation

H.-J. Braun et al.

> 200 mm, < 500 mm

4C < 40° 5.8 Mostly residual moisture; Hot Autumn Drought, heat in Indore, India U – Changes in precipitation patterns in areas will have
coolest quarter mean seedling stage variable effects
minimum temperature and grain fill, SR
> 12°C, < 18°C; wettest
quarter precipitation
> 100 mm, < 400 mm

5A < 40° 3.9 High rainfall/irrigated, Hot Autumn Heat, sprouting, Eastern Gangetic N – Rising temperatures result in large areas becoming
humid; coolest quarter Helmintho- Plains in Nepal, unsuitable for wheat cropping systems and
mean minimum sporium spp., India, agronomy practices allowing early sowing of wheat
temperature > 11°C, Fusarium spp., Bangladesh; paramount; N – Increasing biotic stress; U –
< 16°C in Brazil, Bolivia Londrina, Elevated CO2 may increase water-use efficiency, but
and Paraguay Brazil the same mechanism implies increased canopy
wheat blast temperature, which would be likely to exacerbate
heat stress

5B < 40° 3.2 Irrigated, low humidity; Hot Autumn Heat, SR, LR Gezira, Sudan; N – Rising temperatures result in large areas becoming
coolest quarter mean Kano, Nigeria unsuitable for wheat; N – Increasing biotic stress; U
minimum temperature – Elevated CO2 may increase water-use efficiency,
> 11°C, < 16°C but the same mechanism implies increased canopy
temperature, which would be likely to exacerbate
heat stress

6 > 45° 11.0 Moderate rainfall/summer Temperate Spring Drought, SR, LR, Kazakhstan; P – Rising temperatures allow wheat production in
dominant; high latitude tan spot, Siberia; Harbin, higher latitudes so wheat area expansion likely; P –
45°N; coolest quarter Hessian fly, China Lengthening growing season permits marginal areas
mean minimum FHB, to become productive; P – Reduced risk of winter-kill
temperature < –13°C; photoperiod allows conversion to more productive winter wheat
warmest quarter mean sensitivity
minimum temperature
> 9°C

Facultative wheat
7A < 45° 6.0 Irrigated Moderate Autumn Rapid grain fill, YR, Henan, China U – Reduced cold stress allows growing autumn-sown
cold LR, PM, BYD, spring wheat, possibly reducing yield potential but

Multi-location Testing to Identify Plant Response

CB, LS shortening growing season offering more options for
diversifying cropping systems; P – Reduced
irrigation due to impact of elevated CO2 on water-
use efficiency

7B < 45° 3.0 Irrigated, often only Moderate Autumn YR, CB, LR, SR, Turkey; Iran; U – Reduced cold stress allows growing autumn-sown
supplementary cold LS Central Asia; spring wheat, possibly reducing yield potential but
irrigation Afghanistan shortening growing season offering more options for
diversifying cropping systems; P – Reduced
irrigation due to impact of elevated CO2 on water-
use efficiency; N – Supplementary irrigation with
temporary exposure to drought requires germplasm
that is adapted to ME7 and ME9

8A < 45° 0.2 > 600 mm rainfall; Moderate Autumn YR, Septoria spp., Chillan, Chile U – Reduced cold stress allows growing spring wheat,
medium cold cold PM, FHB, RDC, possibly reducing yield potential but shortening
photoperiod growing season; U – Increasing biotic stress
sensitivity

8B < 45° 0.5 > 600 mm rainfall Moderate Autumn YR, CB, LR, RDC, Transitional U – Changes in precipitation patterns in areas will have
cold PM, sunnpest zones and variable effects; N – Frequency of climate extremes
Trace, Turkey over years increase requiring germplasm with high
yield potential, wide spectrum of disease resistance
and tolerance to drought
Continued

123
 124
Table 7.2. Continued

Latitude Wheat area Temperature Sowing Major biotic and Representative Change in ME due to climate change and conse-
ME (N and S) (million ha) Criteriaa regimeb time abiotic stressesc locations/regions quences for germplasm developmentd

9 < 45° 6.8 Low rainfall < 400 mm, Moderate Autumn Drought, cold, heat West and Central U – Reduced cold stress allows growing spring wheat,
winter/spring rainfall cold at grain fill, YR, Asia; North possibly reducing yield potential but shortening
dominant CB, LR, SR, Africa (mainly growing season; U – Changes in precipitation
sunnpest, RDC, non-dwarf patterns in areas will have variable effects; P –
nematodes cultivars grown) Reduced water deficits through impact of elevated
CO2 on water-use efficiency; N – Rising
temperatures exacerbate water deficits, either
further reducing yields or making production

H.-J. Braun et al.

uneconomical

Winter wheat
10A < 45° 4.6 Irrigated Severe cold Autumn Winter-kill, YR, LR, Beijing, China P – Warmer winters reduce severity of winter-kill,
PM, BYD increasing yields; N – Warmer spring and summer
hasten grain filling; P – Reduced irrigation due to
impact of elevated CO2 on water-use efficiency

10B < 45° 1.6 Often supplementary Severe cold Autumn Winter-kill, YR, Turkey; Iran; P – Warmer winters reduce severity of winter-kill,
irrigation SR, BYD, CB, Central Asia increasing yields; N – Warmer spring and summer
LS, RDC, hasten grain filling; P – Reduced irrigation due to
sunnpest, impact of elevated CO2 on water-use efficiency
Nem

11A > 50° Area in less High rainfall/irrigated, Severe cold Autumn Septoria spp., Central and P – Warmer winters reduce severity of winter-kill
developed long season Fusarium spp., Western
countries YR, LR, PM, Europe; North-
insignificant RDC, BYD west USA

11B < 45° Area in less High rainfall/irrigated, Severe cold Autumn Winter-kill, South-east P – Warmer winters reduce severity of winter-kill
developed short season sprouting, LR, Europe, North
countries SR, PM, FHB, Korea, China
insignificant Septoria spp.,
BYD

12 < 45° 7.9 Low rainfall between 300 Severe cold Autumn Winter-kill, Ankara, Turkey; P – Warmer winters reduce severity of winter-kill; P –
and 450 mm drought, heat West and Reduced water deficits through impact of elevated
during grain fill, Central Asia (in CO2 on water-use efficiency; N – Increased frequency
zinc deficiency, Turkey and Iran of years with severe drought; N – Increased insect
YR, SR, CB, mainly non- problems
sunnpest, Nem, dwarf varieties
RDC grown); China

a Moisture regime refers to rainfall just before and during the crop cycle. High, > 500 mm; low, < 500 mm.
b Temperature regime: hot, mean temperature of the coolest month > 17.5°C; cold, < 5.0°C.
c Biotic stresses: BYD, barley yellow dwarf; CB, common bunt; FHB, Fusarium head blight; KB, Karnal bunt; LR, leaf or brown rust; LS, loose smut = Ustilago tritici; Nem, cereal cyst and

Multi-location Testing to Identify Plant Response

root lesion nematodes; PM, powdery mildew; RDC, root disease complex; SR, stem or black rust; YR, stripe or yellow rust.
d Change in ME: N, negative; P, positive; U, unknown (adopted from Hodson and White, 2007b).

125
126 H.-J. Braun et al.

Table 7.3.  Average sensitivity of cereal yield (expressed as % increase (+) or decrease (–) of current
yields) to temperature increase for maize, wheat and rice derived from 69 papers. Sites were assigned as
either low latitude or mid- to high latitude and the experiments were classified as either with (+) or without
(–) adaptation measures to compensate for temperature increase (see Easterling et al., 2007 for
complete list of references).
Mid- to high-latitude sites Low-latitude sites
Temperature increase (°C) Temperature increase (°C)
Crop Adaptation measuresa 1–2 2–3 3–5 1–2 2–3 3–5
Wheat + 20 18 5 7 –14 –25
– 5 5 –18 –4 –24 –40
Difference 15 13 23 11 10 15
Maize + 10 0 0 6 0 –10
– 0 –3 –9 –7 –20 –35
Difference 10 3 9 13 20 25
Rice + 7 20 6 10 15 0
– 0 5 –9 –2 –8 –20
Difference 7 15 15 12 23 20
a Adaptation measures in these studies were changes in sowing date, changes in cultivar, and shifts from rainfed to
irrigated conditions. Studies span a range of precipitation changes and CO2 concentrations, and obviously vary in how
they represent future changes in climate variability.

2% for rice when temperatures increase by
2°C to 40% for wheat, should temperatures
increase by 5°C. With adaptation measures,
an increase of up to 2°C will raise yield of all
three cereal crops. A 5°C temperature
increase has no effect on rice yields, but will
reduce maize yields on average by 10% and
wheat yields by 25%. For the three crops in
all three temperature scenarios, adaptation
measures will increase yield on average by
10–25% compared to yield without adapta-
tion measures.
A disadvantage of the static definition of
the ME is that it does not take into account
the fact that MEs tend to shift from year to
year and fluctuate in weather patterns. In
particular this is important for locations in
ME2 (high rainfall spring wheat) and ME4
(rainfed spring wheat low rainfall) but also
ME1 (irrigated) and ME5 (irrigated high
temperature). The frequency with which
ME2 or ME4 conditions are experienced
varies between locations. Climate change
may bring an increased intensity and
frequency of storms, drought and flooding,
weather extremes, altered hydrological
cycles, and precipitation (Ortiz et al., 2008).
Such climate vulnerability will threaten the
sustainability of farming systems, particu-
larly in the developing world. Widely
adapted, stress-tolerant cultivars, coupled
with sustainable crops and natural resource
management will provide means for farmers
to cope with climate change and benefit
consumers worldwide.
Wide Adaptation to Buffer Temporal
Climatic Variability in Wheat
The impact of CIMMYT’s wheat breeding on
international collaborative wheat improve-
ment has been discussed by Reynolds and
Borlaug (2006). CIMMYT’s wheat breeding
philosophy and methodology embraces
three important principals: the development
of germplasm with high and stable yield
across a wide range of environments. The
concept of wide adaptation has been criti-
cized, with local or specific adaptation advo-
cated. However, we believe that wide
adaptation to a broad range of environments
becomes increasingly important to develop
cultivars that can cope with the climate
extremes that occur at one location over
years, or with variation within farmers’
fields. For example wheat production in
North Africa often fluctuates year to year
 Multi-location Testing to Identify Plant Response 127
between drought-prone drylands (ME4) and
higher rainfall (ME2) environmental seasons
(D. Hodson, Mexico, 2007, personal commu-
nication).
The international multi-environment
nursery system is the best mechanism to
identify and release spatially widely adapted
wheat cultivars (Rajaram and Ceccarelli,
1998). CIMMYT’s Global Wheat Program
emphasizes the development of wheat culti-
vars with stable yields over a wide range of
environments. Such cultivars, identified
through testing by national agricultural
research systems (NARS) partners in the
International Wheat Improvement Network,
form the genetic basis to further enhance
tolerance to heat and drought stress. The
resolution of this spatial adaptation can be
expressed among geographically distinct
countries and continents to performance
stability across a region, or within a more
local perspective within a farmer’s hetero-
geneous field. In most cases, widely adapted
germplasm is not only input responsive, but
also input efficient (Braun et al., 1996;
Manske et al., 2000). Such performance
stability can also be expressed temporally,
between years.
Climate change will cause major changes
in soil microbial systems and occurrence and
distribution of weeds, insects and diseases
(Easterling et al., 2007). Yield losses from
pest and diseases are an estimated 28% for
wheat, 31% for maize and 37% for rice, and
losses could be as high as 50, 67 and 77%,
respectively, without effective plant protec-
tion (Oerke, 2006). It is likely that more
epidemics will occur in the future when
diseases and pests spread to areas where they
were previously not important. Testing elite
lines in hot spots for a given disease is an
effective way to identify resistant germ-
plasm. This is exemplified by the approach
used to develop wheat lines resistant to
wheat stem rust race Ug99. Most wheat culti-
vars currently grown worldwide are suscepti-
ble to this race. Countries where stem rust is
a potential threat for wheat production have
sent more than 40,000 accessions for evalu-
ation in Kenya and resistant accessions are
now multiplied. Screening at hot spots for
specific diseases, such as North Africa for leaf
rust and Septoria tritici in durum wheat,
Ecuador and West Asia for yellow rust, the
Southern Cone in Latin America for a
complex of diseases including Fusarium head
scab, leaf rust and S. tritici mildew in bread
wheat, Fusarium head scab in China and spot
blotch in the Eastern Gangetic Plains are
paramount to develop widely adapted germ-
plasm buffered against the major biotic
stresses. Pre-emptive breeding (i.e. develop-
ing wheat cultivars that are resistant to a
disease that currently is not present in a
wheat growing zone but could be introduced)
is an important strategy to ensure food secu-
rity. Examples for potential new biotic
threats are discussed in Chapter 4 (Legrève
and Duveiller, this volume).
More than 80% of all freshwater is used
for agriculture, and about 90% of all irri-
gated wheat is grown in less developed coun-
tries (Brown, 2004). The risk to wheat being
exposed to temporary or partial drought
during its growing cycle is consequently
increasing. As the frequency of extremes in
precipitation will increase at given locations,
a location’s wheat production environment
will fluctuate between ME4 (dryland) and
ME2 (high rainfall). A location’s expected
climate is unknown at the time of sowing,
and as a result farmers need cultivars that
are input responsive and productive across a
range of production environments. Cultivars
must be developed that can exploit available
moisture in wetter years combined with
drought tolerance for years that lack opti-
mum levels of precipitation.
CIMMYT develops wheat germplasm that
combines high yield potential under favour-
able conditions, with tolerance to less
favourable drought or water-limiting envir-
onments. Many CIMMYT-derived varieties
have been released for irrigated, rainfed and
drought-prone environments, including
Pavon 79, Seri 82 and PBW343 (Skovmand
et al., 1997). Evidence for their success was
provided by Blum (2005), who, in his review
on breeding for drought tolerance concluded
that it is possible – within biological limits
– to combine drought resistance and yield
potential if selection is designed to recom-
bine a high yield potential genotype with
relevant dehydration-avoidance factors that
128 H.-J. Braun et al.
are not associated with lower yield potential
(e.g. osmotic adjustment).
The main elements of global climate
change, increasing temperature and CO2
concentration, drought, and changes in
disease occurrence and soil microbes will
affect the wheat areas worldwide. The most
severely affected areas will be the lowland
areas in Asia, and the countries of China,
India, Bangladesh, Nepal, Iran, Egypt, Sudan,
Brazil and Paraguay. North African countries
will face yield reductions from extended
periods­of drought. For less developed coun-
tries, the main challenge for wheat breeders
at this stage is selecting genotypes able to
tolerate heat stress and water deficits.
Rice Mega-environments and Climate
Change
Rice, eaten by about three billion, directly
supports more people than any other staple
food (Maclean et al., 2002). Rice adaptation
is affected by many environmental factors,
including day length and temperature, and
soil factors such as salinity, aluminium toxic-
ity and iron toxicity. However, within broad
bands of latitude, rice MEs tend to be defined
in terms of hydrology, water availability and
maximum water depth (Khush, 1984). Rice
is grown in a much wider range of hydro-
logical environments than other crop
species, under conditions ranging from the
basins of poorly drained watersheds where
water accumulates to depths of 5 m or more,
through transplanted paddy fields in which
water levels are maintained at a constant
10–20 cm for most of the growing season, to
upland environments in South-east Asia
where direct-sown rice crops are grown
under aerobic soil conditions on steep hill-
sides. Thousands of years of farmer selection
have resulted in the local development of
specific ecotypes that are adapted to each of
these hydrological environments.
Climate change is likely to affect rice
production in two principal ways: (i) higher
temperatures, both night-time averages
(Peng et al., 2004) and acute high-tempera-
ture stress during flowering, are already
reducing yields in many areas (Wassman et
al., 2009b); and (ii) water availability for irri-
gation is likely to be reduced, and variability
in rainfall may increase the frequency of
both drought and flooding in rainfed
systems. Fortunately, a wide range of genetic
variation for adaptation to both tempera-
ture and hydrological environments exists,
and can be deployed to adapt production
systems to climate change.
The most severe climate change effects
are likely to be those affecting water availa-
bility. Rice environments are broadly charac-
terized as irrigated or rainfed. Irrigated rice
is generally grown in puddled, flooded fields
in which a standing water layer is main-
tained. Because this water is constantly
being lost due to seepage, percolation, evap-
oration and transpiration, irrigated rice
production, which supports the bulk of the
population of Asia, is one of the biggest
users of the world’s freshwater resources
(Tuong and Bouman, 2003). Irrigated rice
systems, although buffered against short-
term variation in water availability, are
extremely sensitive to climate change effects
on surface water availability. Reduced avail-
ability of impounded water or river flows for
irrigated rice production is likely to have a
major impact on irrigated rice production.
The most urgent area requiring adaptation is
likely to be the Indo-Gangetic Plain and the
Indus Basin, where irrigated rice based
primarily on Himalayan snowmelt supports
hundreds of millions of people in India,
Pakistan, Nepal and Bangladesh (Wassman
et al., 2009b). The expected melting of the
Himalayan glaciers (IPCC, 2007) is likely to
greatly reduce irrigation water available in
this critical system, driving shifts to water-
saving production systems (Bouman and
Tuong, 2001) or, in many cases, rainfed
production.
Rainfed rice production areas may also be
affected as climate change increases rainfall
variability, increasing the frequency of
damaging rain-free periods of drought in
some areas, and the frequency of flooding in
others. However, because the current range
of rice production environments already
covers these extremes, adaptation strategies
can be devised based on currently existing
systems. Germplasm that can support these
 Multi-location Testing to Identify Plant Response 129

needed adaptations is available, and can be frequency in a given field, based on its
targeted at critically affected systems toposequence position and soil texture. Yield
through the use of managed stress screening variability under stress can be great even
and extrapolation from METs. It should be within a single field because of its variability
noted, however, that the existence of adapted in soil texture and levelness. This micro-scale
germplasm and accompanying management variability among and within fields results in
systems will not guarantee against product- very large estimates of genotype × environ-
ivity loss; rice systems in which drought or ment interaction and residual error in the
uncontrolled flooding occur are inherently analysis of rainfed rice trials, complicating
less productive than those in which water selection strategies based solely on METs
availability is controlled and no stress occurs, (Cooper et al., 1999). To cope with this vari-
even when adapted germplasm is used to ability, breeders need to use managed stress
mitigate losses. screening protocols that reproduce the range
of hydrologies and water-related stresses
that occur within the TPE they serve.
Breeding for Adaptation to Rice Production strategies for these hydro-
Hydrological Mega-environments logical environments are based on pre-
existing­adapted germplasm. Over time, rice
There are four major hydrological environ- farmers have developed germplasm and
ments for rice production that can be defined management techniques adapted to each of
in terms of toposequence position, or the the hydrological environments described
relative elevation of a rice field within a above (Mackill et al., 1996). In unbunded
watershed consisting of terraced fields that fields at the top of a toposequence, farmers
drain into each other (Garrity et al., 1986), grow short-duration, drought-tolerant
and the resulting effects on the hydrological upland rice varieties established via direct
environment. Within distances of several seeding. Varieties used in these systems are
hundred metres, the toposequence may usually tall, unimproved, and of the aus (in
include: South Asia) or tropical japonica (in South-
east Asia and West Africa) varietal groups.
• unbunded uplands that never retain
In upper bunded fields, farmers tend to grow
standing water;
short-duration, photoperiod-insensitive
• bunded but drought-prone upper fields
modern varieties that flower before the
that retain standing water only briefly
withdrawal of the monsoon, escaping late-
after a rainfall or irrigation;
season drought stress. In well-drained mid-
• well-drained mid-toposequence fields
toposequence fields, farmers usually grow
that receive a reliable supply of water
semi-dwarf varieties developed for irrigated
from fields higher in the watershed, but
systems because of their high yield poten-
that rarely experience stagnant flooding;
tial, and usually establish their crops via
and
transplanting. In lower and flood-prone
• poorly drained lower fields in which water
fields, farmers usually direct-sow tall,
accumulates to depths of 1 m or more
photoperiod-sensitive varieties that flower
during the rainy season.
as the rains cease and thus stagnant water
All four of these hydrological environments begins to decrease (Mackill et al., 1996).
are often found within a small area in rainfed Individual farmers often have fields at
ecosystems. The latter three may also often several toposequence levels, and thus often
be found within a single irrigation command grow several varieties, each adapted to a
area. Water shortage is mainly observed in particular hydrological environment.
unbunded uplands and bunded upper- Improved germplasm has been developed
toposequence fields. Drought stress in these for each of these hydrological MEs. For
environments varies in severity across years unbunded uplands, upland rice varieties
due to variability in the amount and distri- combining high levels of drought tolerance
bution of rainfall, but occurs with predictable­ with improved yield potential and input
130 H.-J. Braun et al.
responsiveness, termed aerobic rice, have
been developed and are used in both rainfed
upland environments and irrigated systems
where it is necessary to reduce water use
(Atlin et al., 2006). These varieties are devel-
oped at IRRI using a selection protocol that
combines testing for yield potential in
aerobic fields where soil water content is
retained near field capacity, with managed
stress trials conducted in the dry season, in
which severe stress is imposed at flowering.
Varieties adapted to upper-toposequence
bunded fields, which must withstand inter-
mittent periods of severe drying, are a major
breeding target for IRRI, and are developed
using managed stress protocols wherein
paddies are drained intermittently through-
out the growing season and then re-flooded
when soil water potentials reach –70 kPA at
20 cm depths. These protocols, conducted at
IRRI’s main research station in Los Baños,
The Philippines, have been highly successful
in identifying germplasm that is broadly
adapted within similar hydrological environ-
ments in different regions.
An important example of specific adapta-
tion to a hydrological stress is submergence
tolerance in rice, a case where a single major
gene is the critical element in an adaptive
trait. On millions of hectares where rainfed
rice is grown by poor farmers, particularly in
eastern India and Bangladesh, rice fields are
subject to flash flooding that completely
submerges plants. Most varieties will not
recover from more than a week of submer-
gence, but several landraces tolerate up to 2
weeks of complete flooding. The key trait
associated with this tolerance is growth
inhibition­ during submergence. Tolerant
varieties become dormant and conserve
carbohydrate reserves, while susceptible
varieties grow rapidly in an effort to exert
leaf tissue above the surface; if they do not
succeed, they exhaust their reserves and die.
Managed stress screening for the trait is
easily accomplished in tanks and deep
paddies that can be drained at will; seedlings
are submerged for 14 days, then the tank or
field is drained and survival is scored. A
highly tolerant Indian landrace, FR13A, was
used as a donor for the trait in genetic
analyses that identified a single major
quantitative­ trait locus (QTL), designated
sub1, which controlled 60–70% of pheno-
typic variation for the trait in the screening
system (Xu and Mackill, 1996). The Sub1
gene has been cloned, and was determined
to code for a defective version of an ethyl-
ene-responsive transcription factor (Xu et
al., 2006). Cloning of sub1 allowed the devel-
opment of gene-based markers for more
accurate genotyping in marker assisted
breeding (MAB). Sub1 has already been
introgressed through MAB into ‘Swarna’, a
widely grown rainfed rice variety that is
highly preferred by farmers in India,
Bangladesh and Nepal, but is highly suscep-
tible to submergence. From project initia-
tion, it took only 2 years to move the allele
for tolerance into ‘Swarna’. The improved
version of ‘Swarna’, ‘Swarna-Sub1’, has a
two- to threefold yield increase over the
recurrent parent after 12–17 days of submer-
gence, and is currently being disseminated
in submergence-prone areas of India and
Bangladesh (IRRI, unpublished data). In this
case, a clear genetic solution to a climate-
induced stress, based on controlled imposi-
tion of stress in the breeding and genetic
analysis process, was available, greatly reduc-
ing the need for multi-location testing for
adaptation to a well-defined TPE. However,
varieties introgressed with sub1 must be
evaluated in METs before release to ensure
that they are adapted and productive under
non-flooded conditions.
Adaptation of Rice to Heat Stress
Adaptation to increasing heat stress is likely
to be more difficult than to changes in hydrol-
ogy, mainly because managed stress screen-
ing is difficult for national breeding
programmes that may not have access to trial
sites at which high temperatures can be reli-
ably expected at appropriate growth stages.
However, Wassman et al. (2009b) noted that
there are several rice-producing regions in
which temperatures during the sensitive
flowering stage exceed 36 or even 40°C.
Germplasm from these areas will serve as an
important source of tolerance in other
regions as average temperatures increase due
 Multi-location Testing to Identify Plant Response 131
to climate change, but mechanisms to make
this germplasm available to other regions
and countries must be strengthened, and
screening and germplasm exchange networks
specifically targeting heat tolerance, which
currently do not exist, must be developed.
Multi-environment Testing Networks
and the Dissemination of Germplasm
to Support Climate Change Coping
Strategies in Rice
As noted above, the range of hydrological
conditions likely to face rice producers
coping with a changing climate already
exists, and is addressed by the breeding
programmes of IRRI and other institutions.
Multi-environment testing and germplasm
distribution networks will be critical to the
rapid dissemination of germplasm adapted
to new hydrological conditions. The coopera-
tive International Network for Genetic
Evaluation of Rice (INGER), managed by
IRRI on behalf of the rice breeding commu-
nity, is the primary vehicle for this dissemi-
nation process. INGER differs somewhat
from other international germplasm
networks coordinated by the Consultative
Group on International Agricultural
Research (CGIAR) centres, in that its focus is
on dissemination of germplasm targeted at
particular MEs, rather than on data collec-
tion.
Given the relative ease with which
hydrological­ MEs can be simulated in
managed stress trials at single locations
within breeding programmes, there has
apparently been less demand by rice breed-
ers for multi-location­testing data. The need
for high-quality data from trials that sample
the TPE directly, however, is increasingly
felt, particularly in breeding for drought
tolerance. This has led to the establishment
of several hydrology-specific collaborative
testing networks, notably the IRRI-India
Drought Breeding Network and the Upland
Rice Shuttle Breeding Network, both of
which are collaborative testing networks
linking IRRI with national breeding
programmes targeting upper-toposequence,
drought-prone environments in India. Such
networks, which usually involve a rather
small group of highly motivated collaborat-
ing programmes, and which meet regularly
to discuss screening techniques and to
exchange and interpret data from collabora-
tive trials, may be preferable to wide-scale
‘box and spreadsheet’ networks (i.e. those in
which the coordinating centre sends out
boxes of packaged seed to collaborators, who
then send back data spreadsheets) in envir-
onments where stress screening is difficult
and the target environment is very clearly
defined in terms of hydrology. They have
proven especially useful in rainfed rice
breeding, and will certainly be needed to
cope with heat stress, which is difficult to
simulate in a managed stress environment.
Screening for Stress Tolerance and
Broad Adaptation in Maize
Maize varietal adaptation to environments
is affected primarily by day length, average
temperature, seasonal rainfall, subsoil pH,
soil N fertility (or fertility management
regime) and characteristic foliar diseases
(Bänziger et al., 2004). At high latitudes, the
requirement to use the full growing season
to maximize yields has led to very precise
targeting of hybrids to bands with similar
accumulation of heat units (Kiniry, 1991),
but in the tropics and subtropics, maize
genotypes are generally broadly adapted
within altitude ranges of around 500 m. Use
of these environmental factors as explana-
tory factors for genotype × environment
interaction of advanced hybrids from METs
to delineate MEs in southern Africa has
resulted in the delineation of six to eight
MEs (Bänziger et al., 2004; Setimela et al.,
2005). Similar combinations of climatic and
edaphic conditions exist within and across
continents, allowing maize MEs to be
approximately identified on the basis of
geographical information system (GIS) data,
and quite accurately predicted when
combined with information on disease prev-
alence. Thus, as climatic conditions change
at particular sites, it will be possible to
132 H.-J. Braun et al.
reassess­ the ME assignment of the site,
guiding­ breeders to appropriate new germ-
plasm. However, environmental variability
remains high within MEs, especially in
developing countries. This is in part due to
management and soil quality variation,
which tends to be very great in agroeco-
systems where commercial and subsistence
producers coexist, and to the frequency of
occurrence of severe abiotic stress, notably
drought, in many areas. This within-ME
variability must be taken into account in
variety evaluation (Bänziger et al., 2004).
Within the commercial maize MEs in
North America, it has been well documented
that genetic gains have resulted largely from
increases in tolerance to a range of stresses
such as drought, low fertility and cold
(Castleberry et al., 1984; Duvick, 1997;
Tollenaar et al., 2000). These increases have
resulted from broad-scale selection within
the TPE via commercial testing networks
sampling dozens or hundreds of locations,
rather than through intentional selection
for tolerance to specific stresses in purpose-
designed screens. However, breeding
programmes in developing countries where
drought is a frequent occurrence rarely have
the resources to operate METs on the scale
required to reliably characterize germplasm
for drought tolerance on the basis of natur-
ally occurring drought. For most stress-
prone TPE, then, information from METs
must be combined with information from
managed stress drought screens to ensure
that, within any reasonable number of
seasons for evaluation of new varieties,
information on stress tolerance can be
obtained.
The design and use of managed stress
environments as a selection tool is complex.
Breeders must take into account the
frequency of occurrence of particular stresses
within the TPE, the precision of yield esti-
mation within a managed stress screen
(broad-sense heritability, or H) and the
genetic correlation between yield in the
screen and yield in the TPE. The genetic
correlation between yield in the screen and
yield in the TPE is difficult to measure and
usually unknown, but for drought-prone
environments, it should not be assumed a
priori to be high. This is because managed
drought screening trials are usually
conducted outside the main production
season, when photoperiod, temperature,
humidity and disease pressures differ from
those in the rainy season. Nevertheless, out-
of-season trials are usually the only possible
option for ensuring the imposition of
drought stress, and are routinely used by the
CIMMYT Global Maize Program under the
assumption that they are predictive of vari-
ety performance in drought events during
the main season.
Yield under drought and low-N stress,
like yield under optimal conditions, is a
highly polygenic trait with low heritability.
In general, the broad-sense heritability or
repeatability (H) is somewhat lower in
managed stress trials than in adjacent, opti-
mally managed trials for both drought and
low-N stress. For low-N stress, Bänziger et
al. (1997) surveyed 14 paired experiments
where the same sets of genotypes were eval-
uated under high- and low-N fertilization
and found mean yields of 5.52 and 2.51
t/ha, respectively. Mean H for yield in the
low-N trials was 0.44, versus 0.62 in the
optimally fertilized trials. For a similar series
of comparisons conducted in managed stress
drought trials, Bolanos and Edmeades
(1996) reported that H for grain yield on an
entry-mean basis in single trials declined
similarly from a mean of about 0.6 under
well-watered conditions to 0.4 under very
severe anthesis-stage stress. Low H for yield
under drought stress is partly a result of the
complexity of screening.
Achieving appropriate stress levels in
early-generation line populations with
diverse flowering dates (because they have
not yet been characterized adequately) is
difficult, with a considerable frequency of
trials failing to differentiate materials due to
excessive or insufficient stress. The problem
of low heritability of yield in drought and
low-N stress trials is compounded within
the CIMMYT maize breeding programme,
from a selection standpoint, by the fact that
new genotypes are evaluated in Stage 1 test-
ing (the preliminary testcross evaluation
step) in only one managed stress trial for
low-N tolerance and one for drought,
 Multi-location Testing to Identify Plant Response 133
whereas they are usually evaluated in three
or more non-stress trials at the same stage.
As a result, precision of estimation of yield
under non-stress conditions is much higher
than under stress, due to greater replication
of the selection unit. Little attention has
been paid to the problem of assigning proper
weights to information from managed stress
trials, which have relatively low precision
due to low levels of environmental replica-
tion, when making selection decisions that
also take into account more highly repeata-
ble means estimated from non-stress trials
conducted across more locations. Methods
for combining data from trials differing in
information content to predict performance
in a target environment are available (Atlin
et al. 2000; Piepho and Möhring, 2005;
Crossa et al. 2006), but these methods
depend on the availability of information on
the frequency of drought within the TPE,
and on an accurate estimation of the correla-
tion between yield in natural droughts and
managed stress environments, which is
rarely available.
Despite the problems and uncertainties
inherent in selection based on combining
data from yield trials conducted under opti-
mal and managed stress conditions, the
CIMMYT maize breeding programme has
demonstrated that this approach is effective
in drought-prone environments in sub-
Saharan Africa. Breeding for drought-prone
and low-fertility environments was initiated
in the 1970s and 1980s, respectively
(Edmeades et al., 1989). Yield under low-N
and drought stress is the focus of CIMMYT
breeding efforts, which integrate data from
multi-location testing under well-fertilized
conditions with phenotypic information on
managed stress screening for yield in severely
N-depleted fields and in managed stress
trials where severe water stress is applied at
flowering. In a series of 97 multi-location
trials conducted over 3 years in eastern and
southern Africa, which yielded less than 3
t/ha due to drought and/or low-N stress, 42
CIMMYT hybrids developed via this proto-
col out-yielded 41 commercial hybrids by an
average of 18% (Bänziger et al., 2006). The
proportionate advantage of hybrids devel-
oped using the CIMMYT managed stress
protocol was greatest in the lowest-yielding
environments. The combined use of managed
stress testing in early generations and multi-
location testing in transnational networks
at later stages has been expanded in sub-
Saharan Africa under the auspices of the
Drought Tolerant Maize for Africa project,
which links CIMMYT’s breeding programme
with national and commercial programmes
in 13 African countries.
As noted for wheat, the CGIAR centres
play an important role in making informa-
tion on germplasm adaptation available
across countries and regions. These networks
are critical in disseminating the germplasm
that will be needed to cope with climate
change, and must be strengthened. MEs
occur across political jurisdictions, but
breeding programme targets, and often their
testing locations, are usually designed with
respect to political realities (Hamblin et al.,
1980), and there is a strong tendency on the
part of breeders managing local or national
programmes to consider data only from
their own testing system. Atlin et al. (2000)
and Piepho and Möhring (2005) demon-
strated that there can be substantial
increases in precision of cultivar evaluation
by incorporating information on perform-
ance at sites outside the mandated TPE of a
breeding programme but within the same
ME.
Breeders’ access to such information
usually ranges from limited to non-existent,
with some important exceptions. For exam-
ple CIMMYT’s regional maize variety testing
networks in eastern and southern Africa
serve many countries that have limited vari-
ety testing capacity, but which contain, in
differing proportions, many of the same
maize MEs. Information from environmen-
tally similar sites outside their jurisdiction is
available to breeders with limited resources
through such METs. However, there are few
such well-managed international testing
networks for maize and other important
crop species that provide breeders with easy
access to analysed and interpreted data and
parental seed of the varieties included in the
trials. Any effort to help impoverished maize
farmers in the developing world cope with
climate change must support both: (i) strong
134 H.-J. Braun et al.
local breeding programmes with extensive
MET networks and relevant managed stress
screening; and (ii) sustained collaborative
international testing networks that allow
breeders access to both germplasm and
information from a wider range of locations
within their MEs, and from MEs into which
their own TPE may shift as a result of climate
change.
Genomic Selection: a Powerful Tool
for Maize Cultivar Adaptation to
Climate Change
New genotyping platforms are coming
on-stream that will rapidly change the nature
of maize cultivar development. These meth-
ods have the potential to greatly facilitate
the process of developing cultivars adapted
to a changing climate, and will increase the
importance of ‘open-source’ multinational
testing networks.
It is estimated that, within maize breed-
ing programmes, approximately between
two and eight haplotypes per gene are
present, and that many of these haplotypes
recur across breeding programmes in differ-
ent frequencies (Ching et al., 2002). A larger
number of haplotypes per gene exists within
the species, but this number is not infinite.
Genotyping platforms are advancing rapidly
in their ability to distinguish large numbers
of haplotypes for dense genetic maps.
A 60,000 single nucleotide polymorphism
(SNP) genotyping array is currently available
for maize that will permit genotyping of
individual lines at high density for approxi-
mately US$200 per sample; the cost per
sample for high-density genotyping is likely
to fall by at least an order of magnitude over
the next few years, while marker density
increases by a similar amount.
The ability to obtain high-density geno-
typic information inexpensively (i.e. for less
than the cost of measuring yield in a single-
location replicated field trial) means that it
will become feasible to genotype at high
density, and with the ability to discriminate
among many alleles, all breeding lines enter-
ing replicated testing, permitting the
on­going estimation of haplotype allele
effects from multi-location trials. Genotypic
value of a line will be predicted, using meth-
ods first outlined by Meuwissen et al. (2001),
from the combined value of marker haplo-
type effects at intervals of 1 cM or less. This
approach, referred to as genomic selection
(GS), essentially treats the haplotype, rather
than the line, as the selection unit.
Simulation studies have shown that GS can
accurately predict breeding values for quan-
titative traits, and the method is rapidly
being applied in animal breeding (Hayes et
al., 2009).
The shift from line to haplotype as selec-
tion unit made possible by GS means that a
line does not need to be evaluated in an
environment to predict its performance in
that environment; rather, performance can
be based on estimates of the effects of the
haplotypes that comprise its genotype, esti-
mated in other environments. For example
if a specific haplotype allele effect is inde-
pendently estimated in different back-
grounds in several different breeding
programmes serving a similar ME (e.g. low-
rainfall subtropics), the value of that allele
can be reasonably extrapolated to other,
similar environments, in which breeding
programmes are likely to be using similar
germplasm. Haplotype effects of alleles in
MEs into which a location or region is likely
to shift due to climate change will also be
available for prediction. Thus, using GS, it
will be possible to: (i) predict the perform-
ance of lines under development for envir-
onments that are likely to occur with higher
frequency in the future due to climate
change; and (ii) rapidly identify, from test-
ing networks in other environments, alleles
that may be useful in coping with new condi-
tions, or conditions that cannot be reliably
tested for, in the TPE. Effective application
of GS as a tool to cope with climate change
will permit the linking of data from different
multi-location testing networks based on
genotypic information. Similar approaches
are likely to be available in most crop species
within the next 5 years.
 Multi-location Testing to Identify Plant Response 135
The Future of Crop Mega-
environments as Breeder Tools
A limitation of the ME concept is its stochas-
tic nature, whereas in reality a given location
will vary temporally from year to year, and
spatially within farmers’ fields and locally.
The combination of water and temperature
defines the occurrence of biotic and abiotic
stresses and the ME concept was very useful
in defining germplasm that has a specific
combination of traits required within a given
ME.
To better target germplasm development
in the future, the ME will need to be refined
to address different needs of the various
production systems. GIS and remote sensing
are powerful tools to classify environments
with biophysical parameters (Hodson and
White, 2007a; Lobell and Ortiz-Monasterio,
2007; Hodson and White, Chapter 13, this
volume) and to estimate probability ranges
for precipitation and use soil parameters
(e.g. micronutrient deficiencies or toxicities
and pH) to characterize environments.
Cooper and Fox (1996) suggested using
probe genotypes as an indirect approach to
characterize environments. Although a limi-
tation of this approach is the dependency
on suitable contrasting genotypes, and
using contrasting genotypes for different
traits may lead to varying environmental
characterization, Mathews et al. (2004) used
pairs of two contrasting genotypes, ideally
iso-lines, for 14 adaptation relevant traits
and identified environment-specific factors
that contribute to environmental classifica-
tion.
Combining remote sensing with model-
ling further enhances the options to classify
environments. Lobell and Ortiz-Monasterio
(2005, 2006, 2007) used modelling and
remote sensing to estimate grain yields and
measure the effect of night and day tempera-
ture on yield. Sutherst et al. (2000) applied
models to estimate the vulnerability of a
given environment for pests and diseases.
It has been suggested that environments
could be classified based on the methods
described in the previous paragraphs, includ-
ing major biotic and abiotic constraints, as
well as other traits important for adaptation
and adoption by farmers (W.H. Pfeiffer,
Colombia, 2009, personal communication).
Considering available genetic variability and
heritability for each of these traits and avail-
ability of markers, the probability and
success rate to find solutions through breed-
ing interventions can be calculated. This
classification will also show in which envir-
onments greatest progress to raise product-
ivity will come from agronomic or
genotype-by-management interventions in
cases where there is no or insufficient genetic
variability for traits of interest. An index can
be developed for important production
systems considering these factors, and even-
tually this will allow setting of priorities and
allocation of resources based on where the
likelihood for successful intervention is
highest.
The ME concept has proved to be very
successful in characterizing major wheat,
rice and maize growing areas and defining
germplasm pools that possess the combina-
tion of traits related to general adaptation
(phenology), tolerance or resistance to the
prevailing biotic and abiotic stresses and
end-use quality characteristics. Since year-
to-year climatic conditions are projected to
become more variable due to climate change
(IPPC, 2007), widely adapted cultivars will
be crucial to buffer unpredictable climate
stresses such as drought, heat and cold,
while being input responsive in years with
agroecological conditions that are favourable
to crop productivity. To identify such culti-
vars, multi-location testing remains the
most efficient system since it allows substi-
tution of temporal with spatial variation.
MEs are defined across continents (Fig. 7.1),
and therefore regional and annual fluctua-
tions in occurrence of abiotic and biotic
stresses cancel each other out. In 1 year, elite
lines can be evaluated in a multitude of
different environments and those best buff-
ered against the highly variable stresses will
be selected for as parents in crossing
programmes and as potential cultivars for
further testing. International evaluation
networks based on exchange of and free
access to germplasm and multi-location test-
ing are therefore a cornerstone in the strat-
egies and efforts to develop wheat, rice and
136 H.-J. Braun et al.
maize germplasm that is adapted to the
increasingly variable growing conditions
encountered due to global climate change.
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 8
Genetic Approaches to Reduce
Greenhouse Gas Emissions:
Increasing Carbon Capture and
Decreasing Environmental Impact

Martin A.J. Parry and Malcolm J. Hawkesford

Abstract
Genetic improvements aimed at increasing crop performance and decreasing the environmental costs
of production are essential to mitigate the impact of climate change. This can be achieved by increasing
production efficiency and decreasing losses during storage and processing thus decreasing the
emissions of greenhouse gases needed to support production. Progress by conventional approaches
may be too small to achieve the necessary progress quickly enough. Biotechnology has the potential to
make larger changes more quickly by both identifying and introducing novel variation in key agronomic
traits. In this chapter we focus on some specific examples of key targets that could be modified by such
directed approaches.

Introduction at or in excess of the worst-case scenarios

The emission of greenhouse gases (GHGs) is
resulting in climate change, which poses
both threats and opportunities to crop
production. It may be possible to escape
some of the adverse effects through changes
in the spatial and temporal patterns of crop
production; however, the difficulties imposed
by changing land use and cultural practices
will mean that there will be an increasing
need for genetic improvement of crops able
to tolerate increasingly stressful environ-
ments, critically often coupled with greater
year-to-year variation. In addition, improved
crops, for example with decreased fertilizer
requirements, increased C capture or shelf
life, may be able to decrease GHG emissions
and thereby mitigate global warming. CO2 is
the most abundant GHG and concentrations
have risen rapidly during the past 250 years
and are expected to continue to do so. Some
scenarios predict a doubling or even trebling
of current CO2 concentrations by the end of
this century; thus far CO2 concentrations
have been increasing and climates changing
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 139
proposed by the Intergovernmental Panel
on Climate Change (IPCC) (2009). Since CO2
is the substrate for the photosynthetic C
assimilatory enzyme Rubisco, the provision
of extra CO2 can be regarded as having a
fertilizing effect. While in the short term,
CO2 fertilization increases photosynthetic
rates of C3 crops (e.g. rice, wheat) in line with
the predictions of photosynthetic models, in
the long term the benefits of additional CO2
fertilization are decreased or lost. In the
short term, higher CO2 concentrations
compensate for the primary enzyme of CO2
assimilation’s (Rubisco’s) weak affinity for
CO2 and for a decrease in the competing
reaction with O2 catalysed by Rubisco, which
in photorespiration leads to the loss in C3
species of approximately 30% of assimilated
C. However, the yield response of C3 crops to
this extra resource is generally much lower
than that predicted by photosynthetic
models, especially in resource-limited condi-
tions (Long et al., 2006a), despite the fact
that elevated CO2 in some species also
extends the potential for C assimilation by
140 M.A.J. Parry and M.J. Hawkesford
delaying reproductive development (Castro
et al., 2009). This results from a decrease in
the amount of photosynthetic machinery, a
downregulation of photosynthetic activity
and, through interactions with other envir-
onmental factors, particularly temperature
and water availability (Moore et al., 1999)
and in some species an accelerated overall
life cycle which mitigates against any exten-
sion of the vegetative phase (Miller et al.,
1997).
The major concerns for crop productivity
as a result of increased levels of greenhouse
gases are related to warmer temperatures
and altered amounts and patterns of rain-
fall. Both average temperature and tempera-
ture variability are predicted to increase.
Average global temperatures are predicted
to increase by 0.6–2.5°C over the next 50
years with significant spatial variation
(IPCC, 2001). While this will permit cultiva-
tion of crops in areas of the world which are
currently too cold (e.g. Siberia and northern
America) and extend the potential growing
season for others, it will also threaten the
viability of crops in many of the major areas
of production. Simulation models suggest
that wheat yields in south-east Australia
may decrease by about 29% (Anwar et al.,
2007) and direct studies in the Philippines
have shown that irrigated rice yields decrease
by 10% for each 1°C increase in the mini-
mum night-time temperature although the
maximum temperature has no effect (Peng
et al., 2004).
Higher temperatures will shorten the life
cycle of most crops, by accelerating develop-
ment and hastening senescence, thereby
decreasing the time available to harvest light
and produce biomass. The effects on phen-
ology vary both between species and with
environment (e.g. David et al., 1997; Remy
et al., 2003; Asseng et al., 2004). Perennial
crops may respond more strongly to an
increased temperature than annual crops
(Estrella et al., 2007). Other effects such as
drought or an increase in ozone concentra-
tions can exacerbate these effects (Porter,
2005). The decreased time available to
harvest light and produce biomass contrib-
utes to yield reductions at elevated tempera-
tures (Estrella et al., 2007).
Higher temperatures increase both dark
and photorespiration. The increase in
photorespiration at elevated temperatures
results both from a decreased ability of
Rubisco to discriminate CO2 from O2 as its
gaseous substrate and an increase in the
solubility of O2 relative to CO2 (Parry et al.,
2003a).
In addition, more frequent, severe and
erratic fluctuations including periods of
extreme temperatures (both high and low)
are predicted. Unlike the effect of CO2 the
yield response to temperature may be discon-
tinuous (Cassman, 2007) and dramatic yield
decreases can occur as a consequence of
small changes in temperature. For example
if critical temperatures are exceeded during
the flowering phase, pollination fails in the
major C3 cereal crops, decreasing seed
production and thus yield. The critical
temperature is 30°C for wheat (Saini and
Aspinall, 1982) and 34°C for rice (Matsui et
al., 1997). Fortunately, there is evidence for
some genetic diversity in this trait that could
be exploited to mitigate the effects of global
warming.
Higher temperatures increase water loss
from both soil and crops thereby increasing
abiotic stress. Conversely, a key expectation
of climate change projections is that elevated
CO2 may decrease stomatal conductance and
thus help mitigate evapotransporative losses
from crops. However, water availability is
already a major determinant of yield. Even
in high-yield environments like the UK the
limited availability of water already decreases
wheat yields by 1–2 t/ha (Foulkes et al.,
2002). Much larger decreases in yield and
even crop failures are occurring and are
anticipated for regions where water avail-
ability is already a major limitation on
production.
Discussion on adaptation to drought and
heat per se can be found in Reynolds et al.
(Chapter 5, this volume). However, even in
those areas in which rainfall is predicted to
increase, yields may be decreased by an
increase in pests and diseases (see Legrève
and Duveiller, Chapter 4, this volume).
Controlling such pests and diseases will
require more energy inputs and thereby
contribute further to climate change.
 Genetic Approaches to Reduce GHG Emissions 141
Targeting Crop Improvement to Adapt
to Climate Change
The simplest approach to dealing with
climate change is the identification of crops
and cultivars already optimized for the new
environments (see Braun et al., Chapter 7,
this volume). However, further optimization
of these crops may still be required to cope
with other issues (e.g. differences in day
length). Since the rate of change of climate is
now faster than at any time (Jackson and
Overpeck, 2000), traditional approaches to
crop improvement may be insufficient to
produce the required new varieties. The need
to identify and introduce additional vari-
ation using wide crosses, mutagenesis or
transgenesis will be essential (see Whitford
et al., Chapter 12, this volume). In this chap-
ter we will focus on some specific examples
of key targets that could be modified by
directed genetic approaches.
C Fixation by Rubisco and the Calvin
Cycle
Photosynthetic CO2 assimilation in crop
plants is not optimal for the current or
Fig. 8.1.  Possible targets to increase net photosynthesis in C3 crops (Long et al., 2006b; Parry et al.,
2007; Reynolds et al., 2009).
predicted future environments (Long et al.,
2006b). The kinetic properties of Rubisco are
widely recognized as a major limitation to
crop productivity. This is not only because of
Rubisco’s weak affinity for CO2 and catalysis
of a competing reaction with O2 but also
because the enzyme has a very low kcat (cata-
lytic rate). High photosynthetic rates there-
fore demand large amounts of Rubisco which
is often more than 50% of soluble leaf protein
and 50% of leaf N. Thus, both crop product-
ivity and the demand for N fertilizer could be
addressed (Fig. 8.1) by overcoming Rubisco’s
manifest inadequacies. This could increase
photosynthetic rates by as much as 100% in
C3 crops (Long et al., 2006b; Parry et al.,
2007; Reynolds et al., 2009) and increase
N-use efficiency (NUE) in both C3 and C4
crops (Ghannoum et al., 2005). While the
advantages of addressing individual parame-
ters are briefly discussed below it is essential
to take into account the overall impact, if
any, of the other kinetic parameters and the
overall costs in terms of both energy and N.
The balance between Rubisco and other
photosynthetic components does not appear
to be correct in C3 crops even under current
conditions (Mitchell et al., 2000). In tobacco,
increasing a single component of ribulose-
142 M.A.J. Parry and M.J. Hawkesford
1,5-bisphosphate (RuBP; a substrate of
Rubisco) regeneration, sedoheptulose-1,7-
bisphosphatase, increased photo­synthesis,
leaf area and plant productivity (Harrison et
al., 1998; Lefebvre et al., 2005; Tamoi et al.,
2006). So it should be relatively easy to
rebalance the investment in photosynthetic
machinery in crop plants with existing tech-
nology.
Rubisco’s weak affinity for CO2 and the
competing reaction with O2 could be partially
overcome by selecting for either natural
variants with higher affinity for CO2 or a
specificity factor (Zhu et al., 2004). However,
Rubiscos with higher affinity for CO2 and a
specificity factor do exist in some species
(Galmes et al., 2005) and these could be
introduced into crop plants; currently
chloroplast­ transformation has only been
developed for a few crop plants and not in
monocots. Even where chloroplast trans­
formation is available, foreign Rubiscos do
not always fold and assemble correctly and
further research is needed to address these
technological challenges (Whitney and
Andrews, 2001; Whitney et al., 2001;
Whitney and Sharwood, 2007).
Considerable benefits could be achieved
by increasing the CO2 concentration at the
active site of Rubisco. The simplest approach
would be to decrease stomatal and mesophyll
conductance, for example by altering phen-
ology of crops to avoid stomatal closure
during drought stress. A more complex alter-
native would be the introduction of C4
metabolism into C3 crops (Hibberd et al.,
2008). However, such a strategy is extremely
complex, requiring the simultaneous intro-
duction of both multiple structural and
metabolic traits into the C3 plant. Negative
impacts of this will be the need to divert light
energy away from the Calvin cycle to the
operation of the C-concentrating mechanism
and the increase in N needed for the proteins
associated with the C4 plant, although this
would be in part offset by a lower Rubisco
requirement pathway. At present this strat-
egy remains at the initial stages of develop-
ment in rice and is therefore a very long-term
option requiring substantial investment.
An alternative approach to decrease the
negative impact of photorespiration is to
decrease the energy required and to increase
the probability of released CO2 being recap-
tured. This can be achieved using metabolic
engineering to introduce genes encoding
proteins that short circuit the photorespir-
atory cycle (Parry et al., 2003b; Kebeish et
al., 2007). One possible negative impact is
the possible accumulation of toxic interme-
diates.
Increasing Amounts of C Fixed Per
Unit Water
An important goal of crop improvement to
decrease GHG emissions and mitigate the
environmental impact of agriculture is to
decrease the gap between yield potential and
actual yield by overcoming the negative
effects on yield of abiotic and biotic stress.
Drought stress has been identified as a major
target. Since the traits important in deter-
mining yield under stress-free environments
are also important in water-limited environ-
ments, the yield potential of crops is strongly
correlated with their performance under
frequent mild or moderate drought stress
(Araus et al., 2002). Yield is a complex multi-
genic trait that can be broken down into its
component traits which relate to crop archi-
tecture, development and phenology, and
these can be selected for in conventional or
marker assisted breeding (MAB). However,
biotechnology has the potential to introduce
new genes, for example to decrease water
loss without decreasing CO2 assimilation by
slightly decreasing stomatal density (Yu et
al., 2008).
Under severe drought, manipulation of
drought responsive genes may be possible to
both ensure survival and sustain yield.
Although many transformations claim to
have created drought tolerance, few, if any,
have generated plants that can sustain high
yields under drought (Parry et al., 2005).
However, recent reports suggest that it may
be possible to combine both characteristics,
for example by manipulating the expression
of transcription factors (Yu et al., 2008; Cao
et al., 2009) or osmoprotectants (Sawahel,
2007).
 Genetic Approaches to Reduce GHG Emissions 143
Yield Components, Sink Strengths,
Implication for N Demands
Ongoing selection programmes will be influ-
enced by climate change as new varieties will
be selected under ambient conditions and
therefore, to an extent, will be the most
appropriate for those conditions. Providing
rates of climate change are not unduly accel-
erated, a consequence will be new and appro-
priate varieties arising within existing
breeding programmes. However, anticipat-
ing change and selecting ideotypes suited
for future climate change is a more secure
and prudent option. In some cases specific
target traits are not those normally directly
selected for, for example C partitioning to
the root (see next section). Future crop
improvement may be targeted at ameliorat-
ing effects of increased CO2 and temperature
or may exploit these conditions to enhance
crop yields. Although there is a primary need
to select for ideotypes responding to progres-
sive climate change, there is an equal import-
ance for selection of yield stability with
increased seasonal variation in weather
patterns, a likely scenario in many regions.
As noted in the introduction, increased
temperatures are likely to accelerate plant
development, including both vegetative and
reproductive growth. Increased tempera-
tures which result in a decreased time to
flowering will limit canopy development and
this is likely to impact on yield. Specifically
in the case of grain crops, decreased post-
anthesis canopy longevity may negatively
affect grain filling. However, while increased
temperatures accelerate grain development
as well as canopy senescence, resulting in a
decreased duration of the grain-filling
period, this may be compensated partially
by increased rates of filling (Nicolas et al.,
1984). A selection of varieties with modified
rates of development, with decreased sensi-
tivity (of development) to increased tempera-
ture or with modified yield components
better able to exploit rapid developmental
progression will be required.
Increased CO2 also impacts on develop-
ment (Springer and Ward, 2007). Photo­
synthetic capacity in excess of sink demand
can lead to excess leaf carbohydrates and
increased hexose cycling, which leads to
decreased expression of photosynthesis-
related genes and initiates senescence
(reviewed in Paul and Foyer, 2001). While
intervention in the signalling processes and
the regulation of senescence would be an
elegant solution, a potentially simpler
approach would be increasing sink plasticity
and capacity, which would minimize the
triggers influencing plant development, thus
improving yields and resource-use efficiency.
An implication of increased photosynthetic
capacity would be a decreased canopy
requirement to achieve the same yield and
consequently a decreased requirement for N
for the development of the canopy.
Increased photosynthesis as a result of
increased CO2 or elevated temperature will
increase yields of photo-assimilate which
ought to lead to increased crop yields. A likely
consequence is an imbalance of tissue C and
N, partially due to dilution of protein N by
increased carbohydrate accumulation. Several
other factors may also contribute to decreased
tissue N, including restricted N uptake aris-
ing from lowered transpiration rates or
greater losses through volatilization or root
exudation (Taub and Wang, 2008). In a study
with current varieties of wheat, barley, rice
and potato, a 10–15% decrease in protein
content was seen at two- to threefold-elevated
CO2 levels (Taub et al., 2008). This was
partially alleviated at higher N availability but
presumably increased efficiency of N capture
would be equally effective. Where insufficient
N availability affects production, clearly,
improved N capture is required; however in
relation to the production of certain crops,
a C-enriched product, for example starch in
feedstocks or biofuels, is highly desirable.
Sink plasticity is a primary target both to
capture the greater potential photo-assimi-
late and to adapt to seasonal weather vari-
ation. For example an older highly tillering
wheat variety was better able to respond to
increased CO2 levels in regard to yield than a
more modern low tillering variety (Ziska,
2008), indicating that some traits which
have been selected against may have value in
reintroduction. This may require accessing
older and more diverse germplasm than is
present in current crop breeding pools.
144 M.A.J. Parry and M.J. Hawkesford
Needs for Increased N Uptake and
NUE
Factors influencing crop production and
yield such as increased photosynthesis (see
above), or determining mineral nutrient
availability (as influenced by rainfall
patterns) will impact on demands for nutri-
ents and efficiency of use; this applies equally
to all nutrients but is exemplified by N, a
major limit on yield and a costly input for
production. As additional N inputs are to be
preferentially avoided for both economic
and environmental reasons, increases in
NUE are preferred. The overall trait of NUE
is the product of two complex subtraits,
namely N uptake efficiency (NUpE) and N
utilization efficiency (NUtE) (Fig. 8.2). NUpE
(N taken up by the crop as a function of the
available N) is a trait associated with root
characteristics of both architecture and
function, including activity of transporters
and assimilatory pathway enzymes. NUtE
(yield of harvested material as a function of
the total N taken up by a crop) is dependent
on canopy functions such as photosynthesis
and nutrient recycling within the plant.
These are independent traits although in
some cases crop height/dwarfism, which will
strongly influence harvest index and utiliza-
tion efficiency, may be related to root growth
(Wojciechowski et al., 2009). In general, each
of these subtraits needs to be independently
selected for in relation to the required crop
ideotype and the anticipated climate condi-
tions of the production regions.
One impact of elevated CO2 may be
increased C allocation to below-ground
material, which ought to enhance both N
and water acquisition ability. Selection for
varieties which are responsive with respect
to such root proliferation capacity will be
beneficial for improving N and water-use
efficiency (WUE), particularly as other
consequences of climate change may be to
reduce water availability and consequently
limit nutrient acquisition. In addition to
this, decreased transpiration and mass flow
brought about by high CO2 will also nega-
tively impact on N acquisition. Crop improve-
ment in root functioning has been suggested
as a possible next Green Revolution (Lynch,
Fig. 8.2.  Possible targets to increase N-use
efficiency (NUE) in crops (see text for explanation).
NUpE, N uptake efficiency; NUtE, N utilization
efficiency.
2007) and will be pivotal for maximizing
water and mineral acquisition in challenging
environments.
Crop Improvement and Mitigation of
Greenhouse Gas Emissions
Agriculture contributes to greenhouse gas
emissions: all agricultural activities require
inputs of energy and will therefore result in
at least CO2 emissions, and additionally
because of the central importance of N in
crop production, ammonia and NOX emis-
sions are also prevalent. In the case of irri-
gated rice production, methane, which is at
least 20-fold more effective than CO2 as a
GHG, can be a significant polluting emission
(Yan et al., 2003). With respect to emissions
from agriculture, the next 50 years will be
the most critical, as anticipated improve-
ments in global agricultural production to
supply the demand of the world population
are expected to be a major driver in climate
change (Tilman et al., 2001). While any crop
improvement directed at yield increases
would theoretically alleviate the detrimental
impacts of crop production if demand was
not increasing, there is likely to be more
activity, in a wider area and utilizing higher
inputs to supply worldwide production
 Genetic Approaches to Reduce GHG Emissions 145
demand. Alleviating environmental impact
is more likely to arise as a consequence of
specifically targeting reduced inputs, for
example in relation to fertilizers or pesti-
cides. Reduced inputs will aid reductions in
emissions, principally those GHGs associ-
ated with energy production and manufac-
turing. In addition reducing N fertilizer
requirements and therefore inputs will have
a substantial effect on ammonia and NOX
emissions. Improving efficiency of use of
other fertilizers will also reduce environ-
mental impacts such as coastal algal blooms
which also result in gaseous emissions (see
Ortiz-Monasterio et al., Chapter 9, this
volume).
Genetic Improvement of Yield
Crop improvement is usually targeted at
improving yields, whether by husbandry or
genetic improvement. Breeding improve-
ments are generally aimed at intrinsic
increases in yield potential or at the allevi-
ation of either biotic (Brown, 2002) or abiotic
(Takeda and Matsuoka, 2008) stresses. As an
example, major improvements in inherent
yield potential of wheat have occurred over
the last 50 years, with the major impact being
the introduction of dwarfing genes (the
‘Green Revolution’), which enhanced harvest
index and avoided the impacts of lodging.
Subsequently, in recent years potential yield
increments for commercial wheats have been
less dramatic although significant.
Yield potentials in breeders’ trials of any
crop seldom translate fully to actual produc-
tion: crops are grown in many varied environ-
ments with differential biotic/abiotic stress
pressures. At the global level conditions are
often suboptimal for crop growth, but even in
intensely managed ideal crop environments,
growers seldom achieve expected yields. The
major biotic stresses are pathogens and pests,
and progress in introducing durable resist-
ance varies between crops. Transgenic
biotechnological approaches, for example Bt
in maize and cotton or herbicide resistance
can have a major impact on pest resistance,
but such approaches remain contentious
(Lemaux, 2009).
Yield improvements are selected by
breeders and adopted by producers and are
usually in conjunction with enhanced patho-
gen/pest resistance or may even be a direct
consequence of this trait. Yield improve-
ments per se will be focused on specific yield
components such as tillering, grain number,
size, etc. or may be developmental attributes
such as early establishment, phenology,
post-anthesis canopy longevity, etc.
It is possible that currently theoretical
yield maxima are being reached and will not
be exceeded unless major breakthroughs in
photosynthetic efficiency can be introduced
(Long et al., 2006b). As noted above, the key
targets are improvements in Rubisco func-
tion (Parry et al., 2007) or the introduction
of C4 photosynthesis into rice (Hibberd et
al., 2008) and other major C3 grain crops. In
the latter case, up to a 50% increase in
photosynthetic efficiency could be achieved,
and given the global dominance of rice as an
essential food, as well as meeting increased
demand, a net result would undoubtedly be
decreased inputs. However, such a strategy
is complex, requiring the introduction of
multiple traits into the C3 plant and, as
observed earlier, at present remains at the
initial stages of development in rice and is a
long-term option.
Genetic Improvement to Reduce
Inputs
Selection for and introduction of pest- and
pathogen-resistant varieties are standard
practices for crop breeders. As already noted,
biotechnological approaches facilitate the
introduction of novel and specific resistance
mechanisms, and are the only mechanisms
for utilizing non-plant genes. Introduction
of herbicide resistance genes via transgene-
sis has been widely adopted and, although
herbicide applications are still required, total
quantities applied are generally lower (see
references in Lemaux, 2009).
Reductions in fertilizer inputs by genetic
improvement have been more difficult,
although by selecting for yield at fixed fertil-
izer inputs (often imposed by legislation
and/or usually a fixed variable in breeding
146 M.A.J. Parry and M.J. Hawkesford
trials), effectively, improvement in fertilizer
efficiency is achieved. This will mainly be a
result of improved utilization efficiency
(production of biomass as a result of nutri-
ents taken up) but increasing efficiency of
capture of nutrients by roots is clearly also a
logical primary target (Fig. 8.2). The obvious
targets are uptake processes, but roots may
have other roles in minimizing N losses from
the soil, for example by inhibiting nitrifica-
tion and thus maintaining organic and
ammonium-N pools which are less subject to
leaching. This is achieved by biological nitri-
fication inhibition genes which are respon-
sible for the trait of exudation of nitrification
inhibitors by the roots. These genes, which
only occur in certain wild species, may be
introduced more generally into cultivated
crops (Subbarao et al., 2007).
Targeting root architecture or function to
enhance nutrient acquisition and minimize
nutrient losses from the soil is a logical
approach to improve efficiency at both high
and low inputs. While acknowledging that
management practices are a major mech-
anism for optimizing uptake efficiency,
improving germplasm to take up more N by
alleviating feedback mechanisms will help
contribute to yield improvements particu-
larly in high-input systems. In contrast, at
low inputs, the benefits to improving capture
are clear and targets include root prolifer-
ation, optimized root exudate production
and expression, and functioning and activity
of ion transporters in the root cells.
Furthermore there is considerable genetic
variation for crop growth at low inputs
(Lynch, 2007).
Developing germplasm with high WUE as
described previously in relation to adapta-
tion to climate change, will also have posi-
tive effects on overall energy usage (avoiding
requirements for irrigation, improving
yields, etc.).
Approaches and Technologies for
Genetic Improvement
Crop improvement needs to be appropriate
for specific circumstances (local cultivation
conditions and practices) as well as targeting
specific crops and end uses of these crops.
The traits involved in yield production and
in efficient resource utilization are complex
and involve many genes. The classical
approach is breeding for phenotypes. Genetic
analysis provides molecular markers to facil-
itate MAB and no knowledge of the precise
mechanisms or specific genes controlling the
traits is necessarily required. Ideally,
however, these markers will be the specific
genes/alleles making a major contribution
to that trait. Identifying and modelling the
important and relevant traits is a prerequisite
to targeted identification of these key genes.
Technologies for identifying new key genes
will exploit facilities offered by genomics
research including transcriptomics (Lu et al.,
2005), traditional quantitative trait loci
(QTL)-based approaches (Habash et al.,
2007) and combinations of these technol­
ogies such as expression QTLs (eQTLs)
(West et al., 2007). Traditional breeding,
using these genes as markers, remains the
key route to improvement, although the use
of TILLING (Targeting Induced Local Lesions
IN Genomes) (Parry et al., 2009) and gene
transformation offer a rapid and targeted
approach which will become important in
the future. A huge wealth of genetic diver-
sity exists even within many modern elite
germplasms (e.g. see Fig. 8.3). However,
research and breeding programmes are
increasingly re-examining older varieties
and landraces or even wild relatives in search
of ‘lost’ alleles which may contribute to
performance under the more stressed condi-
tions that are anticipated.
Ideotypes may be defined for circum-
stances and improvement should be targeted
to achieve these. The ideotypes may include
traits targeted at resource capture, transla-
tion into yield or quality aspects. A net result
will be increased yield and/or reduction in
inputs, resulting in net decreased GHG emis-
sions.
Low-input agricultural systems inevit-
ably have lower emissions associated with
them, although this may not always be the
case and inefficiencies in terms of manage-
ment or available germplasm should be
targeted. Crop ideotypes will be quite specific
for low-input systems and may include
 Genetic Approaches to Reduce GHG Emissions 147
Grain NutE (kg dry matter/kg N) 100
80
60
40
20
0
Varieties of wheat
Fig. 8.3.  Ranked variation in NUtE (yield for N taken up) inLeast
different varietiesdifference
significant
Improvement Network trial at Rothamsted Research from 2004 to 2007 (least significant difference at 5%
level 5.4) (data courtesy of Peter B. Barraclough).
increasing resource capture efficiencies,
particularly at low availability, for example,
of water and fertilizers.
Many routes to crop improvement will be
found by examining diversity in the widest
possible range of germplasm. In some cases,
as already noted, this may require
re-examination­ of wild relatives and
landraces. Bottlenecks in selection may have
been introduced by continued selection in
high-input situations, although this does
not seem to be the case, at least in relation
to N fertilizers and wheat (Ortiz-Monasterio
et al., 1997). Beyond natural variation there
may be circumstances where specific targeted
gene intervention may have a major impact.
Such an example would be the introduction
of the alanine amino transferase gene under
the control of a root epidermal promoter,
which has an effect of improving N capture
efficiency (Good et al., 2007; Shrawat et al.,
2008).
Conclusions/Prospects
Climate change poses both threats and
opportunities to crop production. Even
where it is possible to escape any effects of
climate change by altering spatial or temporal
patterns of production, genetic improve-
ment aimed at improving crop performance
will occur and have an environmental foot-
2004
2005
2006
2007
Mean
grown in the
at Wheat Genetic
5% level 5.4
print. Both conventional and biotechnologi-
cal approaches are necessary to decrease the
impact of agricultural production by increas-
ing the efficiency of production, minimizing
storage losses and decreasing GHG emis-
sions by reducing the need for energy-
intensive­ inputs like N. Considerable
improvements can be made using conven-
tional approaches, especially if they exploit
the widest range of germplasm, including
mutant populations. However, it is far from
certain that the necessary improvements
can be made quickly enough to keep pace
with the changing environment or the polit-
ical pressures to decrease input-related
greenhouse gas emissions. The recent explo-
sion in biological data has provided us with a
much better understanding of many of the
processes involved in the component traits
that underlie complex traits such as yield
and abiotic stress tolerance. Currently much
of this information has only been described
for individual model plants like Arabidopsis.
There is therefore an urgent need to transfer
the technology to crop plants grown in the
field. In many, but not all cases, the appro-
priate technology is available but the remain-
ing hurdles require sustained investment.
Importantly exploitation of the scientific
knowledge will require society to adopt a
more realistic approach to risk analysis and
embrace the new technologies that can
ensure sustainable food security as climate
changes.
148 M.A.J. Parry and M.J. Hawkesford
Acknowledgements
Rothamsted Research receives grant-aided
support from the Biotechnology and
Biological Sciences Research Council
(BBSRC) of the UK. The authors’ research is
also supported by the European Commission
project OPTIWHEAT – Improving the Yield
Stability of Durum Wheat under
Mediterranean Conditions (EC Contract
Number: INCO-CT-2006-015460) and by
the Wheat Genetic Improvement Network,
funded by the UK Department for
Environment, Food and Rural Affairs (grants
AR0709 and IF0146).
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 9
Greenhouse Gas Mitigation in the
Main Cereal Systems: Rice, Wheat
and Maize

Ivan Ortiz-Monasterio, Reiner Wassmann, Bram

Govaerts, Yasukazu Hosen, Nobuko Katayanagi
and Nele Verhulst

Abstract
Population and economic growth are expected to be the main drivers of increased food demand through
2050. This increase in food production will come primarily from intensively managed agricultural
systems. Currently these systems are already important contributors of greenhouse gas (GHG)
emissions. If production practices are not changed in these systems the emission of GHGs is expected
to increase. Therefore, it is important to devise sustainable management practices that, in the short
and long term, will help to reduce the emission of GHGs. This chapter analyses the three main cereal
crops, rice, wheat and maize, and the management strategies that can help reduce GHG emissions. Rice
has the unique characteristic among these cereals of being grown under flooded conditions, which
result in CH4 becoming a particularly important GHG in these systems. Although there remains large
uncertainty in N2O emissions from paddy fields, mid-season drainage has the potential to be an
effective option to mitigate the net global warming potential (GWP) from rice fields when rice residue
is returned to the fields. In the case of wheat and maize cropping systems the adoption of currently
available best management practices for N management should be a good guideline for practices that
reduce N2O emissions. In addition, through the adoption of conservation agriculture it is possible to
reduce GHG emissions by reducing the number of tillage operations and possibly by sequestering C.
Mitigation policies that encourage efficient use of fertilizers, maintain soil C and sustain agricultural
production are likely to have the greatest synergy with sustainable development.

Introduction irrigation, fertilizers and agrochemicals

Driven mainly by population and economic
growth, total world food consumption is
expected to increase over 50% by 2030 and
may double by 2050 (Bruinsma, 2003;
Barker et al., 2007). Most of the increase in
food production in the next decades is
expected to occur through further intensifi-
cation of current cropping systems rather
than through opening of new land into agri-
cultural production (Gregory et al., 2002).
Intensification of cropping systems has been
a highly successful strategy for increasing
food production. The best example is the
well-known success of the Green Revolution,
where the adoption of modern varieties,
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 151
resulted in dramatic increases in food
production. However, this strategy also
resulted in unexpected environmental
consequences, one of them being the emis-
sions of greenhouse gases (GHGs) into the
atmosphere (Matson et al., 1998). Therefore,
future strategies that promote further inten-
sification of agriculture should aim at the
development of sustainable cropping
systems that not only consider increasing
food production but that also look at mini-
mizing environmental impact.
The concentration of GHGs (CO2, CH4
and N2O and halocarbons) has increased
since the pre-industrial revolution years due
to human activities. The atmospheric
152 I. Ortiz-Monasterio et al.
concentration of CO2 has increased from
280 ppm in 1750 to 379 in 2005, and N2O
has increased from 270 ppb to 319 ppb
during the same time period, while CH4
abundance in 2005 of about 1774 ppb is
more than double its pre-industrial value of
750 ppb (Solomon et al., 2007). These gases
absorb light in the infrared regions and thus
trap thermal radiation, which in turn results
in global warming. The global warming
potential (GWP) is a useful metric for
comparing the potential climate impact of
the emissions of different GHGs by express-
ing CH4 and N2O in CO2 equivalents. The
GWP of N2O is 298 times, while CH4 is 25
times that of CO2 in a 100-year time horizon
(Forster, 2007; Solomon et al., 2007).
At present, 40% of the Earth’s land surface
is managed for cropland and pasture (Foley
et al., 2005). The most important cropping
systems globally, in terms of meeting future
food demand, are those based on the staple
crops, rice, wheat and maize. Rice and maize
are each grown on more than 155 million ha
(FAOSTAT, 2009). In addition, rice is the
staple food of the largest number of people
on Earth. The geographic distribution of rice
production gives particular significance to
Asia where 90% of the world’s rice is produced
and consumed (Fig. 9.1). Maize is produced
mainly in the Americas, followed by Asia and
then Africa (Fig. 9.2). Maize is important as a
staple crop (mainly in developing countries)
but it is also important as animal feed and,
increasingly, as biofuel. Wheat is the most
widely grown crop, covering more than 215
million ha around the world, with Asia cover-
ing close to 50% of the world wheat area
(FAOSTAT, 2009; Fig. 9.3).
Mitigation Potential of Agriculture
In 2005, agriculture accounted for an esti-
mated emission of 5.1–6.1 GtCO2-eq or
10–12% of total global anthropogenic emis-
sions of GHGs. Of global anthropogenic emis-
sions in 2005, agriculture accounted for about
60% of N2O (N2O contributed 2.8 GtCO2-eq)
and about 50% of CH4 (CH4 contributed 3.3
GtCO2-eq). Despite large annual exchanges of
CO2 between the atmosphere and agricultural
lands, the net flux is estimated to be approxi-
mately balanced, with net CO2 emissions of
only around 0.04 Gt CO2/year derived from
changes in soil C (Barker et al., 2007).
Without additional policies, agricultural
N2O and CH4 emissions are projected to
increase by 35–60% and ~60%, respectively,
to 2030, thus increasing more rapidly than
the 14% increase of non-CO2 GHG observed
from 1990 to 2005 (Barker et al., 2007).
Improved agricultural management
enhances resource-use efficiencies, often
reducing emissions of more than one GHG.
The effectiveness of these practices depends
on factors such as climate, soil type and
farming system. About 90% of the total
mitigation arises from sink enhancement
(soil C sequestration) and about 10% from
emission reduction. The most prominent
mitigation options in agriculture are shown
in Table 9.1 (according to Barker et al., 2007).
In spite of inherent uncertainties in such
estimates, it can be concluded that the topic
of this review, which addresses the second
option (improved cropland management)
and the fifth option (improved rice manage-
ment), comprises a sizable portion of the
overall mitigation potential of agriculture.
Although the literature provides ample
evidence on the technical feasibility of miti-
gation options in wheat, maize and rice
systems (Matson et al., 1998; Dobermann et
al., 2007; Wassmann et al., 2007), there are
at present no mitigation projects imple-
mented outside experimental farms in the
developing world. In part, this may be attrib-
uted to the exclusion of the land use sector
in the Clean Development Mechanism
(CDM) projects. This stipulation of the
Marrakesh Accords of 2001 may, or may not,
be overturned at the COP15 in Copenhagen
(see Conclusions), so that this review can
also be seen as a timely contribution to the
discussion on potentials and constraints of
mitigation projects in the land use sector.
Rice Systems: CH4 and N2O Mitigation
Rice requires special attention in terms of
GHG emissions due to the unique semi-
aquatic nature of this crop. About 90% of

Greenhouse Gas Mitigation in Rice, Wheat and Maize
Fig. 9.1.  Rice production in East, South and South-east Asia: (a) irrigated and (b) rainfed rice production systems. The rice areas displayed in both maps
comprise approximately 75% of the global rice area.

153
 154
I. Ortiz-Monasterio et al.
Area harvested (ha)

0–100,000

100,001–500,000
500,001–750,000
750,001–1,000,000
1,000,001–3,000,000
3,000,001–5,000,000
5,000,001–28,074,000

Fig. 9.2.  Maize production worldwide 2007 (data from FAOSTAT, 2009; map drawn by Dave Hodson, CIMMYT).

Greenhouse Gas Mitigation in Rice, Wheat and Maize
Fig. 9.3.  Wheat production worldwide 2007 (data from FAOSTAT, 2009; map drawn by Dave Hodson, CIMMYT).

155
156 I. Ortiz-Monasterio et al.

Table 9.1.  Assessing mitigation potentials in agriculture (from Barker et al., 2007).
Million t
Mitigation option CO2-eq/yeara
Restoration of cultivated organic soils 1260
Improved cropland management (including agronomy, nutrient management, tillage/ 1110
residue management) and water management (including irrigation and drainage) and
set-aside/agroforestry
Improved grazing land management (including grazing intensity, increased productivity,   810
nutrient management, fire management and species introduction)
Restoration of degraded lands (using erosion control, organic amendments and nutrient   690
amendments)
Improved rice management   210
Improved livestock management (including improved feeding practices, dietary addi-   260
tives, breeding and other structural changes) and improved manure management
(improved storage and handling and anaerobic digestion)
a Assuming C prices up to US$100/t CO2-eq by 2030.

rice land is, at least temporarily, flooded. The
flooding regime effectively determines all
element cycles in rice fields and represents
the prerequisite for emissions of the major
GHG, CH4. The specific role of rice fields in
the global CH4 budget has also led to several
detailed reviews on this subject (Wassmann
et al., 2004, 2007; Yan et al., 2005; Li et al.,
2006) so the emphasis of this chapter is on
some new insights derived from recently
published data, namely on upscaling and
mitigation.
Flooding of fields is innate to irrigated,
rainfed and deepwater rice, but duration and
depth of flooding varies over a wide range in
these ecosystems. Irrigated lowland rice is
grown in bunded fields with assured irriga-
tion for one or more crops/year. Usually,
farmers try to maintain 5–10 cm of water
(‘floodwater’) on the field. Rainfed lowland
rice is grown in bunded fields that are flooded
with rainwater for at least part of the crop-
ping season to water depths that exceed 100
cm for no more than 10 days. Worldwide,
there are about 54 million ha of rainfed
lowland rice. In both irrigated and rainfed
lowlands, fields are predominantly puddled
(wet tilled) with transplanting as the
conventional method of crop establishment.
In flood-prone ecosystems, the fields suffer
periodically from excess water and uncon-
trolled, deep flooding. About 11–14 million
ha worldwide are flood-prone lowlands. In
many rice production areas, rice is grown as
a monoculture with two crops per year.
However, significant areas of rice are also
grown in rotation with a range of non-rice
crops, including about 15–20 million ha of
rice–wheat systems. The rice–wheat system
comprises nearly 24 million ha of cultivated
land in Asia. In addition, it has the added
complexity that the rice crop is grown under
flooded conditions while wheat requires
well-drained soils. Mitigation strategies for
this system are well covered by Wassmann et
al. (2004). A general summary of the poten-
tial of different management practices in
rice to mitigate GHG emissions can be found
in Table 9.2.
Mechanisms and upscaling
CH4 emission
The magnitude and pattern of CH4 emis-
sions from rice fields is mainly determined
by water regime and organic inputs, and to a
lesser extent by soil type, weather, manage-
ment of tillage, residues and fertilizers, and
rice cultivar. Flooding of the soil is a
prerequisite for sustained emissions of CH4.
Mid-season drainage, a common irrigation
practice adopted in major rice growing
regions of China and Japan, greatly reduces
CH4 emissions. Similarly, rice environments
with an insecure supply of water, namely
Table 9.2. The effect of different management practices on GHG emissions.

CO2 CH4 N2O
Management Status of the Status of the Status of the
Crop practice Effect research Effect research Effect research
Maize and Zero tillage Reduction through fuel use (West Confirmed Reduction through increased More research Increased through increase More research
wheat and Marland, 2002) structure and aeration of needed C and N cycling needed
the soil
Potential reduction through C More research
sequestration (Govaerts et al., needed
2009)
Crop residue Reduction through C Confirmed Reduction through increased More research Increased through increased More research

Greenhouse Gas Mitigation in Rice, Wheat and Maize

retention sequestration (Govaerts et al., structure and aeration of needed C needed
2009) the soil and N cycling
Intensified crop Potential reduction through C More research Potential increase when in More research
rotations sequestration (Govaerts et al., needed rotation with legumes needed
2009)
Timely N fertilizer Reduction through increased Confirmed Reduction through increased Confirmed Reduction through site-specific Confirmed
placement efficiency and reduced efficiency N management, improved
fertilizer use reducing C cost and reduced fertilizer use timing of N application and
for fertilizer production reducing C cost for fertilizer other best management
production practices (Matson et al.,
1998; Snyder et al., 2007)
Intermittent Reduction through increased Confirmed Reduction through increased Confirmed Reduction through increased Confirmed
irrigation WUEa and reduced C cost WUE and reduced fuel cost WUE and reduced fuel cost
for pumping irrigation water for pumping irrigation water for pumping irrigation water
Rice Zero tillage Reduction through fuel use (West Confirmed
and Marland, 2002)
Potential reduction through C More research
sequestration (Govaerts et al., needed
2009)
Crop residue Potential reduction through C Confirmed Increased through higher C Confirmed Site-specific: depending on More research
retention sequestration inputs (numerous citations overall N management needed
possible)
Intensified crop Higher emissions through Site-specific: depending on More research
rotations: shift longer flooding periods background emissions needed
from double to during fallow period which
triple cropping can be high after strong
rainfall
Timely N fertilizer No effect (Wassmann More research Reduction through increased More research
placement et al., 1994) needed efficiency, reduced losses needed
and reduced fertilizer use
Intermittent Reduction through O2 Confirmed Conflicting results; no impact Numerous field
irrigation influx into soils or increase in emissions; observations
(numerous citations possi- postulated link to excessive confirming
ble) N application either no
impact or

157
increase
aWUE, water-use efficiency; GHG, greenhouse gas.
158 I. Ortiz-Monasterio et al.

rainfed rice, have a lower emission potential
than irrigated rice. Organic inputs stimulate
CH4 emissions as long as fields remain
flooded. In addition to management factors,
CH4 emissions are also affected by soil
parameters and climate.
In spite of a growing number of field
experiments on CH4 emissions from rice
fields, the estimates are still attached to
major uncertainties. Intensive field meas-
urement campaigns have clearly revealed
the complex interaction of water regime as
the major determinant of emissions on the
one hand and several other influencing
factors on the other hand. Given the diver-
sity of rice production systems, reliable
upscaling of CH4 emissions requires a high
degree of differentiation in terms of manage-
ment practices and natural factors. Modelling
approaches have been developed to simulate
CH4 emissions as a function of a large
number of input parameters, namely, modal-
ities of management as well as soil and
climate parameters. In spite of considerable
progress over recent years, the available
simulation models for GHG emissions from
rice fields need region-specific validations
before they can be used for reliable compu-
tation of emissions.
All rice-growing nations have signed and
ratified the United Nations Framework
Convention on Climate Change (UNFCCC)
and as part of their commitments all signa-
tories are submitting national inventories of
GHG emissions (NIG) as part of their
National Communications. The UNFCCC
has commissioned the Intergovernmental
Panel on Climate Change (IPCC) to define
guidelines that allow countries to compute
emissions in a comparable fashion. The IPCC
published the original guidelines in 1994
and revised them in 1996 (IPCC, 1997) and
2006 (IPCC, 2006); it has also published
Good Practice Guidance and Uncertainty
Management in National Greenhouse Gas
Inventories (IPCC, 2000). In these efforts to
streamline reporting of NIGs, the land use
sector proved to be especially challenging.
The entire IPCC guidelines are conceived
as fairly simple protocols that allow coun-
tries (called ‘Parties’ in the UNFCCC context)
to compute emission rates even if the level
of information on the different sectors (e.g.
land use) may not be all that detailed. Thus,
it should be stated that these guidelines
cannot be deemed per se as a scientific
approach, but more like a standardized
accounting scheme for emissions.
Nevertheless, effectively all countries have
formed national groups of experts to compile
their NIGs and these have used the most
reliable statistics (e.g. on land use) available
in the respective countries.
The IPCC guidelines distinguish between
activity data, emission factors and scaling
factors (see Table 9.3). The emission factors
distinguish between Tier 1 (a global default
value; to be used as long as there are no
regional measurements available) and Tier 2
(based on emission measurement conducted
in the respective country).
Figure 9.4 displays data obtained from
the EDGAR database (Olivier and Berdowski,
2001; Olivier et al., 2001), in which results
from the NIGs are compiled and extended.
The two maps show CH4 emissions from rice
(Fig. 9.4a) and N2O emissions from cropland
(including rice) (Fig. 9.4b) in South, East and
South-east Asia. To allow comparison of the
emission units of both maps, we have

Table 9.3.  Terminology of IPCC guidelines for emissions from land use (IPCC, 2006).
CH4/rice N2O/crops
Activity data Area of rice land in the respective Amount of N fertilizer used in the
country respective country
Emission factors Amount of CH4 emitted per unit Percentage of N fertilizer emitted
  Tier 1: global default value area as N2O
  Tier 2: regional values
Refinement Specific factors for water Choice of emission factors
management, organic inputs, describing different manage-
etc. ment practices

(a) (b)

Greenhouse Gas Mitigation in Rice, Wheat and Maize

CH4 IN 2000: GWP N2O IN 2000: GWP
EDGAR inventory: rice cultivation EDGAR inventory: arable land

High High

Low Low

Fig. 9.4.  Global warming potential (GWP) (from low to high per 1° grid cell and year) of crop production in South, East and South-east Asia: (a) CH4 emissions
from rice production; and (b) N2O emissions from arable land (rice and other crops). See text for more explanations (map drawn by K. Sumfleth, IRRI).

159
160 I. Ortiz-Monasterio et al.
converted the units of the EDGAR database
into GWP. The CH4 rice map reflects distinct
‘hotspots’ in China and India as well as in
South-east Asia. These hotspots in China,
north-west India, Vietnam and the
Philippines correspond to areas with high
abundance of rice fields and dominance of
irrigated rice. Eastern India, north-east
Thailand and South Myanmar have a rela-
tively high amount of rainfed rice (with a
lower CH4 emission potential than irrigated
rice), but the prevalence of rice as compared
to other forms of land use marks these
regions with high CH4 emission potential.
Yan et al. (2009) recently estimated the
CH4 emissions from the global rice field
based on the Tier 1 method described in the
2006 IPCC guidelines (IPCC, 2006) with
country-specific statistical data regarding
rice harvest areas and expert estimates of
relevant agricultural activities. The estimated
global emission for 2000 was 25.4 Tg/year,
which is at the lower end of earlier estimates
and close to the total emission summarized
by individual national communications.
These results are in line with other assess-
ments of CH4 source strengths from rice
fields. According to the latest summary by
the IPCC (Denman et al., 2007), rice fields
emit 31–112 Tg of CH4/year, about 12–26%
of the anthropogenic CH4 sources, or about
9–19% of the global CH4 emissions (base
years: 1983–2001).
N2O emission
According to the latest IPCC summary
(Denman et al., 2007), arable lands emit
about 2.8 TgN of N2O/year, about 42% of
the anthropogenic N2O sources, or about
16% of the global N2O emissions, but rice
paddy fields are not distinguished from
upland fields. Early studies found N2O emis-
sion from paddy fields to be negligible (e.g.
Smith et al., 1982). However, later studies
suggested that rice cultivation was an
important anthropogenic source of not only
atmospheric CH4 but also N2O (e.g. Cai et al.,
1997).
The initial IPCC guidelines use a default
fertilizer-induced emission factor of 1.25%
of net N input (based on the unvolatilized
portion of the applied N) and a background
emission rate for direct emission from agri-
cultural soil of 1 kg N/ha/year (IPCC, 1997).
Later, the 2006 IPCC guidelines (IPCC, 2006)
revised the emission factor for N additions
from mineral fertilizers, organic amend-
ments and crop residues, and N mineralized
from mineral soil as a result of loss of soil C,
to 1%. In the guidelines, rice paddy fields
have not been distinguished from upland
fields, but Bouwman et al. (2002) reported
on the basis of data published before 1999
that mean N2O emission from rice paddy
fields (0.7 kg N2O-N/ha/year) was lower
than that from upland fields, including
grasslands (1.1–2.9 kg N2O-N/ha/year). Yan
et al. (2003) reported on the basis of data
published before 2000 that the emission
factor for rice paddy fields, at 0.25% of total
N input, was also lower than that for upland
fields, and that the background emission
was 1.22 kg N2O-N/ha/year for paddy fields.
Akiyama et al. (2005) reported on the basis
of data (113 measurements from 17 sites)
published before the summer of 2004 that
the mean N2O emission ± standard devia-
tion and the mean fertilizer-induced emis-
sion factor during the rice-cropping season
were, respectively, 0.341 ± 0.474 kg N/ha/
season and 0.22 ± 0.24% for fertilized fields
continuously flooded, 0.993 ± 1.075 kg N/
ha/season and 0.37 ± 0.35% for fertilized
fields with mid-season drainage, and 0.667 ±
0.885 kg N/ha/season and 0.31 ± 0.31% for
all water regimes. The estimated whole-year
background emission was 1.820 kg N/ha/
season.
Mitigation options
Many mitigation options for GHG emissions
through field management in rice have been
suggested. Yagi (2002) reviewed them for
CH4 emission, broadly dividing them into
four categories (water management, organic
matter, soil amendments and others) and
evaluated them from the viewpoints of
mitigation efficiency, applicability, economy,
and effects on yield, soil fertility and others.
According to the result, the managements
that keep soil conditions more oxidative,
 Greenhouse Gas Mitigation in Rice, Wheat and Maize 161
that allow organic matter decomposition
under more aerobic conditions, and that use
zero tillage seem practical in terms of cost
and labour.
Climate change and competition from
industry and domestic usage will make
stable and adequate supply of water more
difficult even for the irrigated rice ecosys-
tems. Therefore, the mitigation options of
GWP of paddy fields through water
management are particularly relevant.
Mid-season drainage or intermittent
irrigation, which prevents the development
of soil reductive conditions, is considered to
be an effective option for mitigating CH4
emissions from rice fields (e.g. Yagi et al.,
1997; Nishimura et al., 2004). A statistical
analysis of a large data set from Asian paddy
fields indicated that, compared with contin-
uous flooding, a single mid-season aeration
can reduce the average seasonal CH4 emis-
sion by 40%, and multiple aeration reduces
it by 48% (Yan et al., 2005). Li et al. (2006)
estimated that, despite large-scale adoption
of mid-season drainage, there was still large
potential for additional CH4 reductions from
Chinese rice paddies of 20–60% over the
period 2000–2020 according to the
DeNitrification and DeComposition (DNDC)
model, a process-oriented model. Through
the analysis, water management strategies
appeared to be the most technically promising
GHG mitigation alternatives, with shallow
flooding providing additional benefits of
both water conservation and increased
yields. In addition, unflooded rice produc-
tion has been proposed as a potential miti-
gation strategy (see Hobbs and Govaerts,
Chapter 10, this volume).
However, mid-season drainage or
re­­duction in water use increases N2O emis-
sion by creating nearly saturated soil
conditions, which promote N2O production
(e.g. Zheng et al., 2000). There are reports
that mid-season drainage both increased and
decreased the net GWP of paddy fields. Cai et
al. (1999) reported that the GWP of N2O
emissions was even higher than that of CH4
emissions from Chinese paddy fields with
mid-season drainage when large amounts of
chemical fertilizer (364.5 kg N/ha) and farm-
yard manure (5 t/ha) were applied. Bronson
et al. (1997) found that the total GWP of
continuously flooded fields was lower than
that of fields drained mid-season when no
straw was applied, but it was higher when
straw was applied. There seems to be accumu-
lating evidence that mid-season drainage
decreases the net GWP of paddy fields. In
relation to N2O there is a summary of data by
Akiyama et al. (2005) and an estimate using a
statistical model proposed by Yan et al. (2005).
These reports show that mid-season drainage
generally tends to be an effective option for
mitigating net GWP though 15–20% of the
benefit gained by decreasing CH4 emission
was offset by the increase in N2O emission.
Based on the 2006 IPCC guidelines, Yan et al.
(2009) estimated that the increased GWP
resulting from the increase in N2O emission
was only approximately 2.7% of the reduced
GWP through CH4 emission reduction when
all the continuously flooded rice paddies were
drained more than once a rice-growing
season. Li et al. (2004) reported that mid-
season drainage reduces net GWP compared
with continuous flooding; 65% of the benefit
gained by decreasing CH4 emissions from rice
fields in China was offset by an increase in
N2O emissions, as determined by the DNDC
model.
We can conclude that, although there
remains large uncertainty in N2O emissions,
mid-season drainage has the potential to be
an effective option to mitigate the net GWP
from rice fields when rice residue is returned
to the fields. However, there is a risk that
N2O emission offsets reduction of CH4 emis-
sion or moreover brings higher GWP than
CH4 emission when rice straw is not returned
to the fields and when N fertilizer is applied
at a high rate.
The drainage timing and span of the
conventional water management have been
depending on the farmer’s empirical know­
ledge and customary practices. In order to
provide farmers with specific criteria for
draining and watering, Minamikawa and
Sakai (2005) proposed an ‘Eh control’
concept, where water is managed based on
soil redox potential by providing a specific
predetermined lower and upper limit to
reduce CH4 emissions. The International
Rice Research Institute (IRRI) has been
162 I. Ortiz-Monasterio et al.
developing and disseminating the alternate
wetting and drying (AWD) irrigation
management technique as a water saving
technique. The AWD technique provides
farmers with specific criteria of soil water for
judging the timing of watering to avoid
imposing drought stress on rice plants
(Bouman et al., 2007). In addition, AWD
reduces field water application by 15–20%
without significantly affecting yield and
increases the productivity of total water
input (Tabbal et al., 2002; Belder et al., 2004).
Using the concept of ‘Eh control’, IRRI is
trying to develop a new AWD system that
realizes high yield, water-saving and low
GWP compatibly. One of the key prerequi-
sites for the success of this approach will be
the fine tuning of water and nutrient manage-
ment. Excessive N doses trigger pulses of
N2O emissions, and these losses will be exac-
erbated by concomitant shifts in the soil
moisture regime. Thus, AWD should be
closely linked to more precise diagnostics of
N needs. Demand-driven N applications using
leaf colour charts can substantially increase
N-use efficiencies (Dobermann et al., 2002)
and thus reduce N2O emissions by the means
of lower N fertilizer requirements.
Wheat and Maize Systems: Soil C
Sequestration and N2O Mitigation
The main GHGs in wheat and maize crop-
ping systems are N2O and CO2. In the case of
N2O, N fertilizers are a significant direct
source of emissions of this gas in the field
and an indirect source through fossil fuel
energy consumption associated with manu-
facturing and transport of fertilizers. In the
case of CO2 there are expectations that C can
be sequestered through the adoption of
conservation agriculture or no-till systems
(Barker et al., 2007). A general summary of
the potential of different management prac-
tices in wheat and maize to mitigate GHG
emissions can be found in Table 9.2.
N2O
Annual global consumption of N fertilizer
was expected to exceed 100 million t in
2007–2008 (Heffer and Prud’homme, 2007),
while in 1965 it was only 20 million t. During
2006 approximately 70% of that was applied
in developing countries (IFA, 2009). In the
growing season 2006–2006/07 wheat and
maize both contributed 17.3% of world
usage, followed by rice with 15.8%. Together
wheat, maize and rice consume 50% of all N
fertilizer produced around the world (Heffer,
2009). However, only half of the N fertilizer
that is applied in any given field is recovered
in the crop or soil (Matson et al., 1997). The
remaining N can take on many forms, with
various consequences for ecosystems and
public health, before it is ultimately denitri-
fied (the conversion of inorganic N forms to
N2). One of the forms of N that is lost to the
atmosphere is N2O and this is closely
associated­with N fertilized agriculture.
Most N2O originates as an intermediate
product from soil microbial nitrification and
denitrification. A soil’s potential for N2O
emissions increases when the amount of N
available for microbial transformation is
enhanced through N fertilizer application,
cropping of legumes, incorporation of
manures and crop residues, and mineraliza-
tion of soil biomass and other forms of soil
organic material. However, the amounts
emitted depend on interactions between soil
properties, climatic factors and agricultural
practices (Granli and Bøckman, 1994). Most
studies have shown that soil conditions such
as water-filled pore space, temperature and
soluble C availability have a dominant influ-
ence on N2O emissions. Fertilizer source and
crop management factors may affect N2O
emissions, but due to interactions with soil
conditions, it is difficult to draw general
conclusions (Snyder et al., 2007). It is well
established that NO3-N can accumulate in
soils when the N is applied before crop
uptake or when the N rate exceeds crop
demand and the point of crop response
(Legg and Meisinger, 1982). This accumula-
tion of NO3 and NH4, particularly when this
occurs with little or no crop competition for
N uptake, tends to favour the production of
N2O. Therefore, management practices that
avoid or minimize the accumulation of inor-
ganic N, mainly when there is no uptake
competition from the crop, may contribute
to lower emissions of N2O. In this section,
 Greenhouse Gas Mitigation in Rice, Wheat and Maize 163
we will discuss some of those practices.
Granli and Bøckman (1994) and more
recently Snyder et al. (2007) reviewed
management practices that can help miti-
gate N2O emission. We are using those
reviews as our basis for this section and have
complemented them with other literature.
N rate, timing, source and placement
In a number of studies examining spatial
variability, researchers have found that opti-
mal N fertilizer rates vary widely from field
to field (Cerrato and Blackmer, 1991; Schmitt
and Randall, 1994; Bundy and Andraski,
1995). What is probably most important
about N requirements in cereal crop produc-
tion is that the demand changes drastically
from field to field and from year to year. Of
all the information that should be communi-
cated to farmers in any locale is that this
temporal and spatial dependency influences
optimum N fertilizer rates (Raun et al.,
2009).
The current evidence suggests that N2O
emissions are not so much a direct function
of the rate of N applied. Instead, emissions
of N2O seem to be more closely related to N
rates that exceed the N uptake capacity of
the crop over time (Matson et al., 1998; IFA/
FAO, 2001; Snyder et al., 2007). However,
there seem to be some exceptions to this
observation. Zebarth et al. (2008) made N
applications that were at or in excess of crop
N requirement; however, N fertilizer
management practices that reduced rates or
tested split applications did not reduce N2O
emissions. This study provides evidence that
N rate reductions and split applications may
not result in direct reductions of N2O emis-
sions under some conditions (Snyder et al.,
2007).
When trying to identify optimum N
fertilizer rates, soil-testing procedures for
NH4-N and NO3-N are valuable but they
have their limitations. For example when
taken at or near planting they cannot
compensate for subsequent effects of the
environment, especially in winter wheat
that usually spreads over 240 days in its
growth cycle. Sensor-based N management
in wheat and maize is a new technology that
uses an optical sensor, which measures the
normalized difference vegetative index
(NDVI) from wheat and maize canopies. The
use of this vegetative index in conjunction
with an N rich strip (a well-fertilized part of
the field) and a crop algorithm, can be used
to establish the optimum N fertilization rate
(Ortiz-Monasterio and Raun, 2007; Raun et
al., 2009). This technology, which intends to
optimize N rates, minimizes the risk of over
fertilizing. In addition because the diagnos-
tics are done mid-season, N is applied at the
time of high demand by the crop, which in
turn reduces the probabilities of generating
favourable conditions for N2O emissions. An
example of the potential impact of this tech-
nology to identify optimum N rates will be
discussed in the ‘Yaqui Valley case study’
section of this chapter.
Timing of fertilizer application is a criti-
cally important factor in N2O emissions. In
both wheat and maize production systems,
pre-plant application has been documented
as being the most inefficient method of
applying N fertilizer (Mahler et al., 1994;
Randall et al., 2003). Any prolongation of
the period when NH4-based fertilizers can
undergo nitrification or NO3-based fertil­
izers undergo denitrification, without
competition from plant uptake, is likely to
increase emissions of NO and N2O (IFA/
FAO, 2001). This is illustrated by Ortiz-
Monasterio et al. (1996) who compared the
application of 250 kg N/ha (typical farmers’
N rate) in an irrigated spring wheat crop in
the Yaqui Valley of Mexico. Two different
timings were evaluated. One represented
the farmer’s practice which applied 75% of
the total rate pre-plant (20 days before
planting), 0% at planting and 25% at the
time of the first post-plant irrigation
(approximately 45 days after planting). The
second practice did not apply any N pre-
plant, applied 33% of the N at planting and
67% at the time of the first post-plant irriga-
tion. The emissions of N2O in the different
periods are shown in Table 9.4. Using the
same N rate but applying most of the N at
the time of the first post-plant irrigation,
which coincides with the beginning of stem
elongations and is the time of rapid N uptake
by the wheat crop, reduced emissions of N2O
164 I. Ortiz-Monasterio et al.

by more than half. This is in close agreement Slow-release, controlled-release or

with reports from Snyder et al. (2007) who
found that the closer soluble N fertilizer,
such as urea, could be applied to the time
crop N uptake begins, the less potential for
losses as N2O. In addition, Hultgreen and
Leduc (2003) in Saskatchewan, Canada,
showed lower N2O emissions from spring
compared to autumn N fertilizer applica-
tions.
In terms of placement, lower N2O emis-
sions were observed with band placement of
urea (below the surface) near the seed row
compared to surface application (Hultgreen
and Leduc, 2003). Other studies have shown
that shallow placement tends to result in
fewer emissions of N2O compared to deep
placement (Drury et al., 2006). This may be
associated with higher losses of NH3 under
shallow N placement (Snyder et al., 2007).
Granli and Bøckman (1994), after summa-
rizing a number of studies, concluded that
there is no single mineral fertilizer type that
generally gives more N2O emissions than
the others, with the possible exception of
anhydrous NH3, which tends to be associ-
ated with higher N2O emission fluxes. In a
later review, Snyder et al. (2007) cited
Stehfest and Bouwman (2006) who concluded
that after balancing for rate of application,
crop type, climate, soil organic C, soil pH and
length of experiment, differences among
fertilizer types almost disappear.
encapsulated fertilizers
Snyder et al. (2007) in a review of the litera-
ture on mitigation, looked at slow-release
and particularly controlled-release fertil-
izers, as well as stabilized fertilizers that
delay the initial availability or extend the
time of continued availability and controlled
release of fertilizers through a variety of
mechanisms. They found that many of the
results in the literature indicate that
controlled­-release fertilizers are useful for
the reduction of N2O emissions from ferti-
lized soils. However, there are cases where
emissions seemed higher when they were
measured for longer periods. This area merits
more research.
Nitrification and urease inhibitors
Urease inhibitors prevent, for a certain period
of time, the enzymatic hydrolysis of urea,
which depends on the enzyme urease. The
action of nitrification inhibitors is to block or
control conversion of NH4 to NO2 and subse-
quently to NO3. This helps to keep N in the
NH4 longer, encourages NH4 uptake by crops
and prevents N2O emissions from either
nitrification or denitrification (Snyder et al.,
2007). Several synthetic nitrification inhibi-
tors (Nitrapyrin™, DCD™ and Terrazole™) are
available as fertilizer additives (Slangen and

Table 9.4.  Integrated N2O and NO fluxes during three periods: pre-plant to planting (1–30 Nov); planting
to first post-plant irrigation (1 Dec–19 Jan); and after the first post-plant irrigation (20 Jan–21 Feb) (from
Ortiz-Monasterio et al., 1996).
Treatmenta (values in N2O NO Total
Period parentheses are kg N/ha) (kg N2O-N/ha) (kg NO-N/ha) (kg N/ha)
Pre-plant to planting 75-0-25 (187.5) 2.52 5.40 7.92
0-33-67 (0) – – –
Planting to first post-plant 75-0-25 (0) 0.65 0.66 1.31
irrigation 0-33-67 (83.75) 0.48 0.66 1.14
After first post-plant irrigation 75-0-25 (62.5) 0.06 0.23 0.29
0-33-67 (166.25) 0.97 2.05 3.02
Total 75-0-25 (250) 3.23 6.29 9.52
0-33-67 (250) 1.45 2.71 4.16
aFertilizer application (total of 250 kgN/ha): 75-0-25, 75% of the total rate pre-plant, 0% at planting and 25% at the time
of the first post-plant irrigation; 0-33-67, 0% pre-plant, 33% at planting and 67% at the time of the first post-plant
irrigation.
 Greenhouse Gas Mitigation in Rice, Wheat and Maize 165
Kerkhoff, 1984). However, except for certain
niche production systems – the eastern US
Corn Belt and winter wheat areas in North
America – these chemical nitrification inhibi-
tors are rarely effective for other production
systems (Subbarao et al., 2006). Because of
the serious limitations associated with their
functionality and cost effectiveness, these
chemical nitrification inhibitors are not
widely adopted by farmers. Cost-effective
chemical inhibitors that suppress nitrifica-
tion in tropical and temperate production
environments are urgently needed (Ortiz et
al., 2008).
Biological N inhibition
The concept of suppressing nitrification by
releasing inhibitory compounds from plant
roots is termed as biological nitrification
inhibition (BNI) (Subbarao et al., 2005,
2006). Recently Japan International
Research Center for Agricultural Sciences
(JIRCAS) researchers in collaboration with
the International Maize and Wheat
Improvement Center (CIMMYT) discovered
a source for high BNI ability in Leymus race-
mosus, a wild relative of wheat (Subbarao et
al., 2007). A Leymus chromosome contain-
ing the relevant gene(s) was introduced into
wheat, and biological nitrification inhibitors
were also produced and productivity
increased. Further studies, however, are
needed to characterize and quantify the BNI
ability from the wild relative; when further
confirmed, this could open the way for
genetically improving the BNI ability of the
cultivated wheat using wild relatives as a
source for this trait (Ortiz et al., 2008).
Balanced fertilization
There are no studies that have measured
directly the effect of a balanced fertilization
in the emission of GHGs. However, there are
studies that have shown that when P or K
are limiting, N fertilization can not achieve
optimum yields and soil profile NO3 levels
rise, increasing the risk of N losses to the
environment (Snyder et al., 2007).
Tillage systems
There is no clear response, positive or nega-
tive, for the mitigation of GHG emissions
using conservation or zero tillage practices
compared to conventional tillage (intense,
inversion tillage). It appears that in some
regions the benefit of less tillage is an increase
in stored organic matter, both organic C and
organic N, to a greater degree than any poten-
tial increase in N2O emissions, so that the
net GWP decreases. In other studies, the
GWP increases slightly as a result of switch-
ing from conventional tillage to conservation
or no-till (Snyder et al., 2007). This is an area
that requires further research.
The Yaqui Valley case study
The Yaqui Valley is located on the north-west
coast of mainland Mexico in the state of
Sonora. It is bound by the Gulf of California
to the west and the Sierra Madre Occidental
foothills to the north and east. The Valley has
233,000 ha of irrigated intensively managed
agricultural land and has some of the highest
spring wheat yields in the world. The Yaqui
Valley is the home of the Green Revolution
for wheat and one of the first regions to
adopt new cultivars and technologies devel-
oped by CIMMYT, in collaboration with the
Mexican National Program. The Yaqui Valley
is agroclimatically representative of areas
where 40% of the wheat is produced in the
developing world, such as the Indian and
Pakistani Punjab and the Nile Valley in Egypt
among others. Wheat yield trends in the
Yaqui Valley thus represent an important
indicator not only of progress within Mexico,
but of present and likely future growth in
other major developing world wheat systems.
Climate studies in the Yaqui Valley demon-
strated roughly a 10% reduction in yield for a
1°C increment in minimum temperature
(Lobell et al., 2005). In a follow-up study, it
was shown that the apparent historical
importance of minimum temperature mainly
results from covariation between tempera-
tures and solar radiation and not from
greater direct effects of minimum tempera-
ture compared to maximum temperature on
yields (Lobell and Ortiz-Monasterio, 2007).
166 I. Ortiz-Monasterio et al.
A collaborative project between Stanford
University and CIMMYT evaluated the yields,
soil nutrients, gas fluxes and solution losses
of N comparing farmers’ management versus
alternative management practices in the
Yaqui Valley. The farmers’ practice consisted
of the application of 187 kg N/ha of urea to
dry soils 1 month prior to planting, followed
by pre-plant irrigation; an additional 63 kg
N/ha of anhydrous NH3 was applied approxi-
mately 6 weeks following planting. The alter-
native practice added 250 kg/ha N, with 33%
at planting and 67% post-plant. The ‘best’
alternative with respect to reduced N2O and
NO emissions applied a total of 180 kg N/ha,
with 33% at planting and 67% 6 weeks post-
plant. Large reductions in N2O and NOX
emissions and NO3 leaching were possible
with alternative management practices.
Management practices that matched N fertil-
ization with crop demand (i.e. the alternative
practice) reduced combined NOX and N2O
emissions by more than 50% and NO3 leach-
ing by more than 60% without decreasing N
fertilization rates, and further reductions
were possible with the ‘best’ alternative,
which also had lower application rates
(Matson et al., 1998; Riley et al., 2001). None
of the alternative N management practices
resulted in lower income for the farmers. To
understand the processes responsible for
trace gas losses in these systems, 15N-tracer
studies were carried out on N2O flux in the
agricultural fields. The results of this work
suggested that denitrification plays a critical
role in N2O and N2 losses in the period imme-
diately following irrigation or in periods
following rains, when soil-water-filled pore
space reached over 80%. However, those data
also showed that at lower levels of soil mois-
ture, nitrification is the more important
source of N2O as well as of NO. During the
4-week period of high emissions both
processes contributed equally to total N2O
losses (Panek et al., 2000). This emphasizes
the fact that we should not only worry about
the build-up of soil NO3 levels but also of
NH4.
In the Yaqui Valley, fertilizer is the main
cost of production for wheat; therefore, the
impact of increased fertilizer efficiency on
budgetary savings to the farmers was evalu-
ated. In contrasting the farmer practice with
the ‘best’ alternative (which matched N
supply with demand and applied lower N
rates) in terms of reduced trace gas losses and
total N losses, it was found that the alterna-
tive resulted in savings equivalent to
12–17% of after-tax profits from wheat farm-
ing in the valley (Matson et al., 1998). Despite
the apparent win–win management alterna-
tive, which reduced N losses (including N2O)
to the environment and improved farmers’
income, later surveys indicated that few of
the farmers adopted the alternative. To better
understand this issue an N-management
decision model was developed for an irrigated
wheat system that incorporates hypothetical
diagnostics of soil N and growing season
climate. The model was then used to quantify
the potential value of these forecasts with
respect to wheat yields, farmer profits and
excess N application. Under farmers’ manage-
ment (i.e. no diagnostics), uncertainty in soil
and climate conditions was shown to account
for an average over-application of N by
roughly 35%. Both soil diagnostics and
climate forecasts were shown to increase
profits significantly and decrease over­-
application of N, with minimal changes in
yield (Lobell et al., 2004). Therefore, perhaps
the greatest barrier to adoption of the ‘best’
alternative was the high degree of spatial and
temporal variability in fertilizer require-
ments.
To address the issue of spatial soil N vari-
ability in the Yaqui Valley CIMMYT and
Oklahoma State University worked on the
development and validation of a new tech­
nology. This included the use of N-rich strips
together with the GreenSeeker™ sensor and a
crop algorithm in farmers’ fields with the ulti-
mate goal of improving N-use efficiency
through site-specific N management in irri-
gated spring wheat. During the wheat crop
cycle 2002/03 and 2003/04, 13 validation
experiments of approximately 1 ha each were
established in farmers’ fields in the Yaqui
Valley. After the validation phase, during the
wheat crop cycle 2005/06, eight technology
transfer trials were established in farmers’
fields; these had on average an area of 10 ha
each. Both the validation and the technol­
ogy transfer trials compared the farmers’
conventional N-management use versus the
use of the N-rich strip together with the
 Greenhouse Gas Mitigation in Rice, Wheat and Maize 167
GreenSeeker™ sensor and a crop algorithm to
derive N recommendations for each individ-
ual field. The results of the validation trials
showed that on average, over all locations,
farmers were able to save 69 kg N/ha, with-
out any yield reduction. At the price of US$0.9
per unit of N in the valley when these experi-
ments were established, this represented
savings to the farmers of US$62/ha. Previous
research suggests that a significant reduction
in the emissions of N2O is taking place as well
(Matson et al., 1998). The technology transfer
trials demonstrated that, in large commercial
areas with an average size of 10 ha, farmers
could improve their farm income by
US$50/ha when using sensor-based N
management. The adoption of this technol-
ogy allowed farmers to obtain significant
savings in N use and thus in farm profits.
Farm income was increased by US$56/ha,
when averaged over all trials in all years
(Ortiz-Monasterio and Raun, 2007). Since
the crop cycle 2005/06 the technology trans-
fer effort has continued with similar levels of
savings. Given that the sensor is relatively
expensive (US$4500) the technology transfer
work has been based around farmers’ unions.
These unions provide credit and access to
lower cost inputs to farmers in the Yaqui
Valley. The technical departments of these
unions have purchased the sensor and provide
the N diagnostic service to member farmers.
The development of a ‘pocket’ sensor is well
advanced and the first prototypes will be
available for testing in the Yaqui Valley for the
crop cycle 2009/10. The estimated cost of this
new sensor will be around US$100, which will
change the dynamics of the transfer of this
technology in the valley and in other areas
around the world. Currently, there are experi-
ments taking place in wheat-growing areas in
India, Pakistan, China, Argentina, Turkey and
Uzbekistan for the calibration and validation
of this technology.
C sequestration in maize and wheat
cropping systems
The global C cycle is constituted by a short-
term biochemical cycle superimposed on a
long-term geochemical cycle. Annually,
anthropogenic activities distort both cycles
by emitting 8.6 Pg C, which is absorbed by
the atmosphere (3.3 Pg C), the oceans (2.2
Pg C) and unknown sinks (Lal, 2007). The
soil C pool comprises two components: (i)
the soil organic carbon (SOC) pool; and (ii)
the soil inorganic carbon (SIC) pool.
Agricultural activities affect mainly the SOC
pool, which constitutes a potential source of
GHGs with estimated current C content in
the 1 m top layer two times larger than the
atmospheric pool (Lal, 2007). The global C
and N cycles are connected.
Farming alters the C cycle and manage-
ment of cropping systems will determine the
amount of CO2 emissions in the atmosphere
as well as the potential for C sequestration
in the soil. Marland et al. (2003) distin-
guished four sources of CO2 emissions in
agricultural systems: (i) plant respiration;
(ii) the oxidation of organic C in soils and
crop residues; (iii) the use of fossil fuels in
agricultural machinery such as tractors,
harvesters and irrigation equipment; and
(iv) the use of fossil fuels in the production
of agricultural inputs such as fertilizers and
pesticides. Therefore, C sequestration in soil,
C storage in crop residues and CO2 emissions
from farming activities should be consid-
ered, as well as the hidden CO2 costs of
energy use and C emissions for primary
fuels, electricity, fertilizers, lime, pesticides,
irrigation, seed production and farm machin-
ery (Wang and Dalal, 2006), to evaluate the
atmospheric CO2 mitigation capacity of
different farming practices.
C levels in soil are determined by the
balance of inputs, as crop residues and
organic amendments, and C losses through
organic matter decomposition. Management
to build up SOC requires increasing the C
input, decreasing decomposition, or both
(Paustian et al., 1997). The C input may be
increased by intensifying crop rotations,
including perennial forages and reducing
bare fallow, by retaining crop residues, and
by optimizing agronomic inputs such as
fertilizer, irrigation, pesticides and liming.
Decomposition may be slowed by altering
tillage practices or including crops with
slowly decomposing residue in the rotation.
168 I. Ortiz-Monasterio et al.
Tillage can influence bulk density of the
topsoil. Ellert and Bettany (1995) therefore
suggested basing calculations of SOC stocks
on an equivalent soil mass rather than on
genetic horizons or fixed sampling depths in
order to account for differences in bulk
density.
To better understand the influence of
different management practices (with special
emphasis on tillage, crop rotation and resi-
due management) on C sequestration,
Govaerts et al. (2009) did an extensive litera-
ture review. Some of the already existing
reviews on the influence of agriculture and
management on C sequestration were used
as a basis and the review was completed
through a further literature search.
The influence of residue retention on SOC
stocks
Crop residues are precursors of the SOC
pool. The decomposition of plant material to
simple C compounds and assimilation and
repeating cycling of C through the microbial
biomass with the formation of new cells are
the primary stages in the process of humus
formation (Collins et al., 1997). Returning
more crop residues can be associated with an
increase in SOC concentration (Govaerts et
al., 2009).
Furthermore, the decomposition rate of
organic material is controlled by the quality
of the substrate that is available for soil
microorganisms (Mosier et al., 2006). The
C:N ratio is one of the most often used
cri­teria for residue quality (Vanlauwe et al.,
1994), together with initial residue N, lignin,
polyphenols and soluble C concentrations
(Trinsoutrot et al., 2000; Moretto et al.,
2001). As decomposition proceeds, the recal-
citrant components will accumulate in the
material. Due to this change in organic-
matter quality, the decomposition rate of
fresh plant litter may decrease and it can
thus be expected that when residues are
retained the decomposition rate and CO2
flux will decrease over time. The quality of
the substrate is, besides the recalcitrant
components, also determined by the nutri-
ent composition of the organic material
(Lavelle et al., 1993).
It has often been reported that during
the decomposition of organic matter, espe-
cially when organic material with a large C:N
ratio is added to soil, decomposition may
limit microbial activity and thereby decrease
the CO2 flux (Lavelle et al., 1993).
The influence of tillage practice on SOC
stocks
The largest contribution to reducing the CO2
emissions associated with farming activities
is made by the reduction of tillage oper-
ations. Reduced tillage practices influence
greatly the use of fossil fuels by agricultural
machinery as well as the electricity consumed
in the production, the transportation and
the reparation of the machines. In a wheat–
fallow system in semi-arid subtropical
Queensland, Australia, practising zero till-
age reduced fossil fuel emissions from
machinery operation by 2.2 million g
CO2/ha over 33 years or 67 kg CO2/ha/year
(four to five tillage operations with a chisel
plough to 10 cm during fallow each year were
replaced by one herbicide spray) (Wang and
Dalal, 2006). West and Marland (2002)
reported estimates for C emissions from
agricultural machinery averaged over maize,
soybean and wheat crops in the USA of 69.0,
42.2 and 23.3 kg C/ha/year for conventional
tillage, reduced tillage and zero tillage,
respectively. Robertson et al. (2000) studied
fields under maize–wheat–soybean rota-
tions in the Midwest, USA and calculated
slightly lower fuel costs for zero tillage
systems than for conventional tillage. While
enhanced C sequestration will continue for a
finite time, the reduction in net CO2 flux to
the atmosphere, caused by the reduced
fossil-fuel use, can continue indefinitely, as
long as the alternative practice is continued
and could more than offset the amount of C
sequestered in the soil in the long term
(West and Marland, 2002).
Govaerts et al. (2009) evaluated most of
the available case studies on C sequestra-
tion. Based on the review of research
constraints for C sequestration the authors
decided to include only those results that
came from measurements done to at least
30 cm deep after at least 5 years of continuous­
 Greenhouse Gas Mitigation in Rice, Wheat and Maize 169
practice. In seven of the 78 cases retained,
the soil C stock was lower in zero compared
to conventional tillage, in 40 cases it was
higher and in 31 of the cases there was no
significant difference. Results do not always
point in the same direction. Doran et al.
(1998) report a positive effect of zero tillage
on SOC stocks, whereas Halvorson et al.
(2002) and Thomas et al. (2007) did not find
a significant difference between zero and
conventional tillage, and Black and Tanaka
(1997) even reported a negative effect from
a conversion to zero tillage. There is no
consensus between the studies in wheat–
fallow systems reported about the effect of a
conversion to zero tillage on SOC stocks.
West and Post (2002) for example found
that moving to zero tillage in wheat–fallow
rotations showed no significant increase in
SOC and, therefore, may not be a recom-
mended practice for sequestering SOC.
Conversely, Alvarez (2005) reported in his
compilation study that soils from wheat–
fallow (n = 13) under reduced and zero till-
age had a mean SOC content that was 2.6 t
C/ha higher than under conventional tillage,
an increase similar to that for the other rota-
tions. The mechanisms that govern the
balance between increased or no sequestra-
tion after conversion to zero tillage are not
clear, although some factors that play a role
can be distinguished, for example soil physi-
cal properties, such as soil aggregation, bulk
density and porosity, root development and
rhizodeposits, baseline soil C content,
climate, landscape position and erosion/
deposition history.
It is known that aggregation physically
protects soil organic matter that would
otherwise decompose rapidly (Beare et al.,
1994; Six et al., 2002). Due to more stable
macro-aggregates in zero tillage compared to
conventional tillage (Six et al., 2000), the soil
organic matter is more trapped inside the
soil aggregates and therefore not accessible
to microbial action (Beare et al., 1994; Six et
al., 2000). Tillage brings microorganisms in
direct contact with crop residue, thereby
increasing decomposition. Additionally, till-
age disrupts aggregates liberating physically
stabilized organic material (Buchanan and
King, 1992; Six et al., 2002). Each tillage
operation will thus induce a flush in C miner-
alization and subsequent C loss. Lal (2004)
reported that conventional tillage increased
the emission of CO2 by 30–35 kg C/ha
compared to zero tillage.
Crop root-derived C may be very import-
ant for C storage in soil (Holanda et al., 1998;
Flessa et al., 2000; Gregorich et al., 2001;
Tresder et al., 2005; Baker et al., 2007 all as
cited in Govaerts et al., 2009). Zero tillage
practices can produce greater horizontal
distribution of roots and greater root density
near the surface (Ballcoelho et al., 1998; Qin
et al., 2006).
VandenBygaart et al. (2002) concluded
that soil erosion and redistribution over a
prolonged period also affects SOC storage
under zero tillage. Soils that had lost SOC
through soil erosion had a high potential to
gain SOC when converted from conventional
tillage to zero tillage, whereas in depressed
landscape positions (with high SOC from a
history of soil deposition) the potential to
gain SOC was lower when converted to zero
tillage, with some soils even losing SOC.
The influence of crop rotation on SOC stocks
Altering crop rotation can influence soil C
stocks by changing the quantity and quality
of organic matter input. Increasing rotation
complexity and crop intensity is expected to
increase the SOC stocks. In the literature
review reported by Govaerts et al. (2009)
however, the soil C stock increased in 28 of
the 55 retained cases, showed no significant
difference in five cases and decreased in 22
cases. West and Post (2002) calculated from
a global database of 67 long-term experi-
ments that enhancing rotation complexity
(i.e. changing from monoculture to continu-
ous rotation cropping, changing crop–fallow
to continuous monoculture or rotation crop-
ping, or increasing the number of crops in a
rotation system), did not result in seques-
tering as much SOC (15 ± 11 g C/m2/year)
on average as did a change to zero tillage, but
crop rotation is still more effective in retain-
ing C and N in soil than monoculture (Yang
and Kay, 2001). The increased input of C as a
result of the increased productivity due to
crop intensification will result in increased
170 I. Ortiz-Monasterio et al.
C sequestration. VandenBygaart et al. (2003)
reported in their review of Canadian studies
that, regardless of tillage treatment, more
frequent fallowing resulted in a lower poten-
tial to gain SOC in Canada. Also eliminating
fallows by including cover crops promotes
SOC sequestration by increasing the input
of plant residues and providing a vegetation
cover during critical periods (Franzluebbers
et al., 1994; Bowman et al., 1999), but the
increase in SOC concentration can be
negated when the cover crop is incorporated
into the soil (Bayer et al., 2000). Crop resi-
due mass may not be the only factor in SOC
retention by agricultural soil. The mech-
anism of capturing C in stable and long-term
forms might also be different for different
crop species (Gál et al., 2007).
Conservation agriculture: the combined
effect of minimum tillage, residue retention
and crop rotation on SOC stocks
Conservation agriculture is defined as a
cropping system that combines the follow-
ing principles: (i) reduction in tillage; (ii)
retention of adequate levels of crop residues
on the soil surface; and (iii) use of crop rota-
tions. These conservation agriculture prin-
ciples seem to be applicable to a wide range
of crop production systems under low-yield-
ing, dry rainfed and high-yielding irrigated
conditions. Obviously, specific and compat-
ible management components (weed control
tactics, nutrient management strategies and
appropriately scaled implements) will need
to be identified through adaptive research
with active farmer involvement to facilitate
farmer adoption of appropriate conserva-
tion agriculture-based technologies for
contrasting agroclimatic/production systems.
Therefore, by applying the three components
conservation agriculture has the potential to
increase C stock through the increased input
from crop residue retention, increased crop
intensifications and crop rotation and the
reduced C decomposition through reduced
tillage.
The soil C case study results reported in
Govaerts et al. (2009) are not conclusive.
More research is needed, especially in the
tropical areas where good quantitative infor-
mation is lacking. The mechanisms that
govern the balance between increased or no
sequestration after conversion to zero till-
age are not clear, although some factors that
play a role can be distinguished (e.g. root
development and rhizodeposits, baseline
soil C content, bulk density and porosity,
climate, landscape position and erosion/
deposition history). However, even if C
sequestration is questionable in some areas
and cropping systems, conservation agricul-
ture remains an important technology that
improves soil quality, controls erosion and
reduces tillage-related production costs.
Conclusions
Increasing food production – especially in
the developing world – is imperative for the
well-being of the present and future gener-
ations of poor farmers and consumers.
Although we do not deny the urge for curtail-
ing GHG emissions, the authors are
convinced that any conceivable programme
on mitigation of GHG emission from the
agricultural sector has to be based on the
premise of higher food production. As for a
future agreement after the rather disap-
pointing outcome of the United Nations
climate change Conference of Parties
(COP15) in Copenhagen, it will be crucial to
converge the legitimate goals of increasing
food security and reducing GHG emissions.
As long as food security is not com-
promised by GHG mitigation, the common
denominator for mitigation options is the
increase in resource-use efficiencies. This
paradigm applies to all three cereal systems
discussed in this chapter and, arguably, to
the agricultural sector as a whole. The adop-
tion of currently available best management
practices for N management should be a
good guideline for practices that reduce N2O
emissions. However, what is regarded as a
good agricultural practice varies somewhat
from region to region, reflecting variations
in local soils and climatic conditions.
We can conclude that, although there
remains large uncertainty in N2O emissions
from paddy fields, mid-season drainage has
potential to be an effective option to mitigate­
 Greenhouse Gas Mitigation in Rice, Wheat and Maize 171
the net GWP from rice fields when rice resi-
due is returned to the fields. However, there
is the risk that N2O emission offsets reduc-
tion of CH4 emission or, moreover, brings
higher GWP than CH4 emission when rice
straw is not returned to the fields and when
N fertilizer is applied at a high rate.
A common conclusion for all three crops
is that it is necessary to generate more data
sets where simultaneous measurements of
CH4, N2O and CO2 emissions are collected
together with C sequestration data to be able
to better estimate the net GWP of wheat,
maize and paddy fields.
Many agricultural mitigation activities
show synergy with the goals of sustainabil-
ity. Mitigation policies that encourage effi-
cient use of fertilizers, maintain soil C and
sustain agricultural production are likely to
have the greatest synergy with sustainable
development (Barker et al., 2007). However,
the link between sustainability (conserva-
tion agriculture) and GHG emissions is a
complex one and the balance between C
sequestration, leaching losses and GHG
emission needs to be carefully considered
and analysed. This is an area in great need of
additional research.
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10
How Conservation Agriculture
Can Contribute to Buffering
Climate Change

Peter R. Hobbs and Bram Govaerts

Abstract
Agriculture contributes significantly to greenhouse gas (GHG) emissions: CO2, CH4 and N2O.
Promoting agricultural practices that mitigate climate change by reducing GHG emissions is important;
but those same practices also have to improve farmer production and income and buffer the production
system against changes in climate. New agricultural practices also need to prevent further soil
degradation and improve system resilience. Conservation agriculture (CA), based on minimal soil
disturbance, permanent ground cover and crop rotations is a management system that achieves these
goals; it results in improved soil physical and biological health, and better nutrient cycling and crop
growth. CA also increases water infiltration and soil penetration by roots, which allows crops to better
adapt to lower rainfall and make better use of irrigation water. Water and wind erosion are also
reduced by CA since the soil surface is protected and water runoff is lowered as more water enters the
soil profile. CA can also help to mitigate climate change. Growing rice with less water and adopting CA
practices results in less CH4 emission. However, care has to be taken with fertilizer management to
minimize N2O emissions that can increase under resulting aerobic conditions. CA can also substantially
reduce CO2 emissions through reduced diesel use and increased sequestration of C in the soil. This
chapter recommends that integrated research and participatory extension are needed to fine-tune CA
to specific locations to convince farmers to adopt this technology.

Introduction most of the additional 23% of anthropogenic

Agriculture contributes significantly to
greenhouse gas (GHG) emissions including
CO2, CH4 and N2O. The recent International
Panel on Climate Change (IPCC) synthesis
report on climate change (IPCC, 2007) indi-
cates that agriculture contributes 13.5% of
the 49 Gigatonnes (Gt = 109 t) of annual
global GHG emissions due to human activi-
ties in 2004. Figure 10.1 shows the contribu-
tion of various sectors of human activities to
GHG emissions in 2004. Note that agricul-
ture is separated from forestry, which also
includes deforestation. CO2 was the major
anthropogenic GHG with 77% of emissions
in 2004 (Fig. 10.2). CH4 (23 times global
warming potential (GWP) of CO2) and N2O
(310 times GWP CO2), when expressed in
terms of CO2 equivalents, accounted for
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 177
GHG emissions. Agriculture contributes
about 50 and 70% of total anthropogenic
emissions of CH4 and N2O, respectively
(IPCC, 1996).
The three main GHGs are produced in
many ways in agriculture. When soils are
tilled the organic matter in the soil is exposed
to O2 and is broken down and releases CO2.
Much of the tillage is also done by tractor:
ploughing uses diesel to power the equip-
ment and in the process releases CO2. Diesel
is also the source of energy in planting seeds,
powering mechanical irrigation pumps,
cultivating weeds and when combine
harvesters are used to harvest the crop.
Transportation of inputs (fertilizer, pesti-
cides, etc.) and outputs (grain, fodder or
residues) from agriculture also consumes
diesel and releases CO2. Therefore, to
178 P.R. Hobbs and B. Govaerts

Fig. 10.1.  Percentage contribution of different human interventions in greenhouse gas emissions in 2004
in CO2 equivalents (adapted from IPCC, 2007).

Fig. 10.2.  Percentage contribution of different anthropogenic greenhouse gas emissions in 2004 in CO2
equivalents (adapted from IPCC, 2007).

evaluate­ the atmospheric CO2 mitigation
capacity of different farming practices, C
sequestration in soil, C storage in crop resi-
dues, as well as CO2 emissions from farming
activities should be considered together
(Wang and Dalal, 2006). To include farming
activities, estimates must be made of energy
use and C emissions for primary fuels, elec-
tricity, fertilizers, lime, pesticides, irriga-
tion, seed production and farm machinery
(West and Marland, 2002).
CH4 emissions come from natural and
human activity and have a total value of 528
Tg/year (Tg = 1012 g), with human activity
CH4 estimated to be 370 Tg/year, the major
contributors being anaerobic rice cultivation
(80 Tg/year or 22%), enteric fermentation in
animal production (93 Tg/year or 25%) and
burning of biomass (40 Tg/year or 11%)
(Houweling et al., 1999). Enteric fermenta-
tion in animals is an important considera-
tion as nations get wealthier and their
populaces demand more meat products
(Verge et al., 2008); however, this falls out of
the scope of this chapter and will not be
discussed.
N2O is the third most important GHG
with both natural and anthropogenic
sources. It is estimated that 376.7 Tg CO2
equivalents/year were released in the USA in
 Conservation Agriculture Buffering Climate Change 179
2003 (US Emissions Inventory, 2006) with
67% of these N2O emissions coming from
agricultural soil management. N2O emis-
sions are related to denitrification of nitrates
in soils under wet and anaerobic conditions.
Published papers report both increasing
(Mackenzie et al., 1997; Ball et al., 1999) and
decreasing (Kaharabata et al., 2003; Drury et
al., 2006; Patiño-Zúñiga et al., 2009) N2O
emissions with various management options
on various soil types. This is an important
topic to discuss because any gains in reduc-
ing CO2 emissions with conservation agri-
culture (CA) must not be lost by increased
N2O emissions.
Promoting agricultural practices that
mitigate climate change by reducing GHG
emissions is important, but those same
practices also have to improve farmer
production and income and buffer the
production system against the effects of
changes in climate. The overall impacts
predicted by climate change models vary,
but we are now locked into global warming
and inevitable changes to climatic patterns
that are likely to exacerbate existing rainfall
variability and further increase the frequency
of climatic extremes (IPCC, 2007). Where
excess rain occurs, extreme rainfall events
will increase leading to flooding and soil
erosion. In low rainfall, drought-prone areas,
there is general acceptance in the science
community of more frequent moisture stress
because of failed rainfall patterns and
increased evaporation caused by higher
temperatures (Cooper et al., 2008). In Africa
specifically, the projected combined impacts
of climate change and population growth
suggest an alarming increase in water scar-
city for many countries, with 22 of the 28
countries considered likely to face water
scarcity or water stress by 2025 (UNECA,
1999). This in turn will curtail the ability of
irrigated agriculture to respond to the
expanding food requirements of tomorrow’s
Africa. This raises the spectre of a worsening
food security crisis (Rosegrant et al., 2002).
Evidence of changes in climate extremes,
in particular of temperature, is already
emerging in southern and West Africa (New
et al., 2006). Ortiz et al. (2008) modelled the
possible effects of temperature change on
wheat productivity in the major wheat-
producing environments of the world. Their
climate scenarios suggest that global warm-
ing may be beneficial for the wheat crop in
some regions, but could reduce productivity
in zones where optimal temperatures already
exist. For example, by 2050, as a result of
possible climate shifts in the Indo-Gangetic
Plain – currently part of the favourable, high
potential, irrigated, low rainfall mega-
environment­ – as much as 51% of its area
might be reclassified as a heat-stressed,
irrigated­, short-season production mega-
environment. This shift would represent a
significant reduction in wheat yields; the
Indo-Gangetic Plain accounts for 15% of
global wheat production.
In order to cope with the increased climate
risk, agricultural systems will have to be more
robust and resilient to buffer for extreme
weather events such as drought, flooding, etc.
It is paramount that new agricultural prac-
tices not only prevent further soil degrad­
ation but also improve system resilience
through increased soil organic matter,
improved water-use efficiency as well as
nutrient-use efficiency, and increased flora
and fauna biodiversity. However, the manage-
ment of agriculture to cope with GHG emis-
sions and the negative effects of climate
change on food production lies in the hands
of farmers, pastoralists and forest managers
whose decisions are determined by multiple
goals. In this chapter we will discuss the
promotion, extension and adoption of agri-
cultural practices like CA that mitigate by
reducing GHG emissions and help adapt to
climate change. The major potential for CA as
a climate mitigation strategy is based on its
related agronomic and economic productivity
gains. The additional benefits from the partial
or full adoption of CA are generally substan-
tial even in the absence of incremental profits
arising from market or subsidy payments for
soil conservation or GHG mitigation credits.
CA has that win–win combination of being a
soil and water conservation technology that
can also increase productivity. Higher yields
in wheat and maize (Govaerts et al., 2005) are
the result of an increase in soil quality, espe-
cially in the topsoil (Govaerts et al., 2006b).
Increased aggregation and soil organic matter
180 P.R. Hobbs and B. Govaerts
at the soil surface lead to increased water- and
nutrient-use efficiency (Franzluebbers, 2002)
as well as reduced soil erosion (Verhulst et al.,
2010). The increased production and profita-
bility can be the major driving factor for farm-
ers to implement CA and thus, go beyond
ineffective and expensive direct incentives
(Govaerts et al., 2009a). This chapter will
discuss in more detail some of the benefits of
CA and explain why it is important for future
food production while at the same time help-
ing to buffer against global climate change.
Conservation Agriculture
For centuries, farmers have used tillage for
agricultural production. There were several
reasons for adoption of tillage including the
oxidation of the organic matter to release
needed nutrients for crop production.
Farmers also used tillage to make it easier for
them to plant seed into the ground, to manage
crop residues and organic amendments, and
to control weeds, pests and diseases. With the
introduction of mechanical power and trac-
tors tillage became even more widespread
and manufacturers developed various imple-
ments such as mould board and disc ploughs
that inverted the soil. However, it soon
became apparent that intensive tillage
resulted in various negative effects on the
environment. The soil was more exposed to
climatic events leading to erosion and loss of
topsoil. A good example of this was the dust
bowl in the USA in the 1930s. Farmers used
mould board ploughs to bury the native
grasses and prepare the soil for crop produc-
tion. This exposed the soil surface to rain and
wind. The result was the dust bowl with large
quantities of topsoil removed by wind and
washed away by water. Conservation tillage
was introduced to remedy this problem. In
conservation tillage only minimal ploughing
is done to make it easier to plant seed with
the available seed drills. Conservation tillage
also leaves previous crop residues on the soil
surface to protect it from wind and rain. A
minimum of 30% soil cover is required to be
called conservation tillage, a major manage-
ment practice in US farming today.
Conservation tillage still results in soil
disturbance in the surface layers. This
disturbance affects both the physical and
biological properties of the soil. CA goes one
step further and reduces the surface tillage
to a minimum. ‘Conservation agriculture’ is a
term coined by the Food and Agriculture
Organization (FAO) in the last two decades
and has three important pillars (FAO, 2009):
1. Reduction in tillage: the objective is to
achieve zero tillage, but the system may
involve controlled tillage seeding systems
that normally do not disturb more than
20–25% of the soil surface; aims are to reduce
soil disturbance, energy use and production
costs and to increase profitability.
2. Retention of adequate levels of crop resi-
dues and surface cover on the soil surface:
the objective is the retention of sufficient
residue on the soil to protect the soil from
water and wind erosion; aims are to reduce
water runoff and evaporation, to improve
water productivity and to enhance soil physi-
cal, chemical and biological properties asso-
ciated with long-term sustainable
productivity. The amount of residues neces-
sary to achieve these ends will vary depend-
ing on the biophysical conditions and
cropping system.
3. Use of crop rotations: the objective is to
employ diversified crop rotations to help
moderate/mitigate possible weed, disease
and pest problems; aims are to utilize the
beneficial effects of some crops on soil condi-
tions and on the productivity of subsequent
crops, and to provide farmers with economi-
cally viable cropping options that minimize
risk.
There are many reports describing the
benefits of CA (Hobbs et al., 2008). Wear and
tear on farm equipment is decreased as a
result of less use. Diesel use for land prepar-
ation is significantly less. The benefits also
include better and more stable yields through
timelier planting or buffering of moisture
stress, reduced production costs, improved
soil physical and biological properties,
improved water infiltration, less soil and
wind erosion and a potential for biological
control and less disease and pest incidence.
The CA principles are applicable to a wide
range of crop production systems from low-
yielding, dry, rainfed conditions to high-
yielding, irrigated conditions. However, the
 Conservation Agriculture Buffering Climate Change 181
techniques used to apply the principles of
CA will be very different in different situ-
ations, and will vary with biophysical and
system management conditions and farmer
circumstances. Therefore, there are various
forms of CA. Specific and compatible
management components (pest and weed
control tactics, nutrient management strat-
egies, rotation crops, appropriately scaled
implements, etc.) will need to be identified
through adaptive research with active farmer
involvement. Applying CA essentially means
altering literally generations of traditional
farming practices and implement use. As
such, the movement towards CA-based tech-
nologies normally comprises a sequence of
step-wise changes in cropping system
management to improve productivity and
sustainability.
In South Asia the term ‘resource conserv-
ing technologies’ has been coined to describe
some of these intermediate steps towards
the complete implementation of all the CA
principles. Resource-conserving technolo-
gies can be applied on both flat and raised-
bed planting systems. For example under
gravity-fed irrigated conditions, a raised-bed
system with furrow irrigation may be more
suitable than planting on the flat since the
furrow system will allow irrigation water to
be managed more efficiently. Therefore, a
first step will be to implement a convention-
ally tilled raised-bed system as a resource
conserving technology in preparation for
the next step, permanent raised beds. The
permanent raised-bed system uses the same
principles as CA but first forms a bed and
furrow system which is then kept perman-
ent, with only minimal soil disturbance and
reforming of the beds, if needed, after each
crop. The crops are planted on top of the
beds and a layer of crop residue is left as in
CA planted on the flat. There are several
advantages to permanent beds including
improved water productivity as well as
‘controlled traffic’ since the compaction
associated with tractor wheels is restricted
to the furrows between beds where plants
are not drilled (Sayre, 2005).
As soil tillage is primarily used for weed
control, this has been a major concern in
adopting zero tillage and CA systems. Tillage
systems often induce changes in composi-
tion of weed species and densities. Weeds
are often initially greater when farmers shift
to zero-tillage systems and this is one of the
few negative aspects of CA; essentially, farm-
ers substitute herbicides for tillage. Zero till-
age often favours perennial (broadleaf and
grass) species compared to conventional till-
age (Carter et al., 2002) as tillage destroys
and prevents these plants from setting seed,
but zero tillage has been reported to success-
fully control annual broadleaf weeds over
time when the right weed control practices
are implemented and the seed bank gets
depleted by not tilling (Arshad et al., 1998).
In South Asia, where zero-tillage wheat is
planted after rice, the grassy weed Phalaris
minor germinates less because of less soil
disturbance (Hobbs and Gupta, 2003). Also,
the mulch residue cover can control weeds
by excluding light (Ross and Lembi, 1985).
The introduction of herbicide-tolerant crops
such as soybeans, maize, cotton and canola
has helped to reduce the problems of weeds
associated with zero tillage in many coun-
tries where CA has significant acreage. In this
case, glyphosate, a broad-spectrum herbi-
cide, is used to control weeds in combination
with herbicide-tolerant crops (Roundup
Ready™ crops). Additionally, crop rotation,
one of the other pillars of CA, leads to diver-
sification of cropping practices and therefore
changes weed populations and species
composition, leaving less opportunity for an
individual weed to become dominant.
Permanent ground cover is a critical
aspect of CA. Results from rainfed and irri-
gated long-term trials (> 10 years) in Mexico,
show that not zero tillage as such, but the
combination of zero tillage with the reten-
tion of sufficient soil-surface crop residue
resulted in increased physical, chemical and
biological soil quality. Moreover, the data
show that zero tillage without residue reten-
tion resulted in soil degradation beyond the
conventional tillage practice (Govaerts et al.,
2005, 2006a, b, 2007a, b; Limon-Ortega et
al., 2006). Ground cover can be provided in
various ways; probably the easiest way is to
leave the anchored residues from the
previous­ crop. It has been found that this
anchored residue does not create a problem
182 P.R. Hobbs and B. Govaerts
for planting the subsequent crop. The height
at which the crop residue is cut will deter-
mine the quantity of straw left on the field.
This can be an issue in dryland agriculture
where crop yields are low and the residue left
after harvest is not sufficient to provide
ground cover. There are also issues where the
crop residues have other uses. For example
in some countries the crop residues are
removed and used as feed for animals. In
this case farmers may not leave enough resi-
dues in the field to obtain successful CA. In
these areas solutions have to be found to
increase the overall biomass productivity of
the system in order to meet all farmer and
soil needs. Improved fodder sources should
also be part of the improved management
package (Govaerts et al., 2005; Verhulst et
al., 2010). Another way to provide perman-
ent soil cover is to grow a cover crop. This is
a crop that is grown for its biomass rather
than any grain yield. After the crop has
reached sufficient size it is knocked down or
killed but is not incorporated into the soil.
The cover crop can be leguminous and help
fix N or can be another crop species that
provides good biomass. Introduction of
cover crops can however be very challenging
in some environments, depending on the
climate conditions and the difficulty in
convincing a farmer to grow a crop that will
not give any immediate economic return.
Permanent soil cover is important for
several reasons (Verhulst et al., 2010).
Results from two long-term trials estab-
lished in the early 1990s in different agro-
ecological systems in Mexico clearly show
the importance of crop residue retention on
soil aggregation (Fig. 10.3). The two systems
were: (i) a low-input, semi-arid, rainfed
system in the rainfed central highlands
(2240 m above sea level) with zero tillage on
the flat; and (ii) a high-input, arid, irrigated
system in the north-western part of the
country with zero-tilled permanent raised
beds. Since organic matter is a key factor in
soil aggregation, the management of previ-
ous crop residues is a key to soil structural
development and stability. It has been
known for many years that the addition of
organic substrates to soil improves its struc-
ture (Ladd et al., 1977). The presence of crop
residues over the soil surface prevents aggre-
gate breakdown by direct raindrop impact as
well as by rapid wetting and drying of soils
(LeBissonnais, 1996). Moreover, aggregates
are more stable under zero tillage with resi-
due retention compared to conventional till-
age and zero tillage with residue removal
(Carter, 1992; Chan et al., 2002; Filho et al.,
2002; Hernanz et al., 2002; Pinheiro et al.,
2004; Li et al., 2007 – all as cited in Verhulst
et al., 2010 and Govaerts et al., 2009b). Soil
macro-aggregate breakdown has been iden-
tified as the major factor leading to surface
pore clogging by primary particles and
micro-aggregates and thus to formation of
surface seals or crusts (LeBissonnais, 1996;
Lal and Shukla, 2004). Under permanent
soil cover wind erosion and rapid wetting
(i.e. slaking) result in less aggregate break-
down, preventing surface crust formation
(LeBissonnais, 1996; Scopel and Findeling,
2001; Lal and Shukla, 2004). As a result
infiltration of water is generally higher in
zero tillage with residue retention compared
with zero tillage with residue removal (Fig.
10.4). In addition, the residues left on the
topsoil act as a barrier, reducing the runoff
velocity and giving the water more time to
infiltrate; the residue intercepts rainfall,
absorbs its energy and releases it more
slowly for infiltration into the soil. The
‘barrier’ effect is continuous, while the
prevention of crust formation probably
increases with time (Scopel and Findeling,
2001). The increased aggregate stability and
reduced runoff result in lower soil erosion in
CA (Carter, 1992; Chan et al., 2002; Filho et
al., 2002; Hernanz et al., 2002; Pinheiro et
al., 2004; Li et al., 2007; Govaerts et al.,
2007c – all as cited in Verhulst et al., 2010
and Govaerts et al., 2009b). The biomass is
also a source of food for microbes including
various bacteria, fungi, nematodes, earth-
worms and arthropods. The residue retained
on the soil surface provides residue-borne
pathogens and beneficial soil microflora
with substrates for growth. This can induce
major changes in disease pressure in CA
systems. However, functional and species
diversity are increased, creating more possi-
bilities for integrated pest control. The effect
of CA on soil mesofauna is variable, but in
 Conservation Agriculture Buffering Climate Change 183

(a)
3.5

3.0

Mean weight diameter (mm)

2.5

2.0

1.5

1.0

0.5

B b A a
0
Removal Full retention

Residue management

(b)
2.5
Mean weight diameter (mm)

2.0

1.5

1.0

0.5

C b AB b B b A a
0
Burning Removal Partial Full retention
retention

Residue management

Fig. 10.3.  The effect of residue management on soil aggregate distribution and stability expressed as the
mean weight diameter (mm) obtained by dry sieving (grey bars) and wet sieving (white bars) in the zero-
till treatments of (a) the long-term rainfed sustainability trial in the highlands of Central Mexico (described
in Govaerts et al., 2005), and (b) the long-term irrigated sustainability trial in Ciudad Obregón, North
Mexico (adapted from Limon-Ortega et al., 2006). Differences between values of the presented
parameters were tested for significance using least square difference grouping and treatments with
different letters within the same typography differ significantly at P < 0.05. Bars indicate standard error.
184 P.R. Hobbs and B. Govaerts
120
100
Time-to-pond (s)
80
60
40
20
0
c b ab
Burning Removal Partial
retention
Residue management
Fig. 10.4.  The effect of residue management on
time-to-pond (s) in the zero-till treatments of the
long-term irrigated sustainability trial in Ciudad
Obregón, North Mexico during the wheat phase of
the rotation (adapted from Verhulst et al., 2009).
Differences between values were tested for
significance using least square difference grouping
and treatments with different letters differ
significantly at P < 0.05. Bars indicate standard
error.
general macrofauna abundance is stimulated
(Verhulst et al., 2010). This biological activ-
ity is also critical for improving nutrient
cycling and improving surface soil physical
properties. The biological activity combined
with the previous crop’s root channels results
in interconnected soil pores that lead to
improved water infiltration (Kay and
VandenBygaart, 2002). This is important for
reducing water erosion and increased stor-
age of soil moisture in the soil profile.
Conservation Agriculture as a
Climate Change Adaptation Strategy
As mentioned earlier, CA improves the soil
physical and biological properties. Several of
the effects of CA for different systems are
summarized in Table 10.1. The resulting
improved soil quality and improved nutrient
cycling will improve the resilience of crops to
adapt to changes in local climate change. The
minimal soil disturbance and soil cover will
protect the biological component of the soil
and help with biological tillage, keeping
pests and diseases under control through
biological diversity processes and making
nutrients available to plants for good
growth.
One of the major effects of global climate
change will be changes in rainfall patterns.
In some locations this could mean less rain
and more droughts, while in other areas
there may be more intensive rains and
increased erosion of soils. CA can definitely
a help in water harvesting and reduce soil loss
Full through wind and water erosion and evap-
retention oration compared to conventional tillage
and zero tillage with residue removal. The
combination of reduced tillage and perman-
ent soil cover has been shown to increase
water infiltration compared to a tilled soil
(Hobbs et al., 2008) allowing farmers to
have more efficient water harvesting and
moisture available in the soil profile for crop
growth (Fig. 10.5). There are numerous
studies that show infiltration of water in a
zero-tillage and surface mulch system is
superior to that of a bare tilled soil (Verhulst
et al., 2010) (see Table 10.1). These papers
also show that erosion is reduced in CA that
combines reduced tillage and residue reten-
tion. Also, soil water-holding capacity will
increase because of improved soil organic
matter leading to increased soil moisture
available during the crop season (Kemper
and Derpsch, 1981; Fabrizzi et al., 2005)
(Table 10.1). Azooz and Arshad (1995)
found higher soil water contents under zero
tillage compared with using a mould board
plough in British Columbia. Mupangwa et
al. (2007) determined the effect of mulch-
ing and tillage on soil water content in a clay
and a sandy soil in Zimbabwe. Mulching
helped conserve soil water in a season with
long periods without rain at both experi-
mental sites. Soil water content consistently
increased with increase in surface cover
across the three tillage practices (planting
basins, ripper tine and conventional
plough). Soils under zero tillage with resi-
due retention generally had higher surface
soil water contents compared to tilled soils
in the highlands of Mexico (Govaerts et al.,
2007a). In general, in rainfed conditions
tillage and residue management signifi-
cantly affect crop yields during years of poor
rainfall distribution (Johnson and Hoyt,
 Conservation Agriculture Buffering Climate Change 185

Table 10.1.  Overview of different cropping systems (conservation agriculture and conventional practices)
that result in an increase in key soil parameters.
System that results in
an increase for the
Parameter selected parametera Details of system Reference
Soil aggregation CA Zero tillage + residue Govaerts et al. (2009b)
and structural
stability
CA = CONV. TILL. Minimum till + residues Hulugalle et al. (2006)
CA Minimum till + residues Hulugalle et al. (2007)
CA Zero tillage + residue Kennedy and Schillinger (2006)
CA Permanent raised beds + residues Govaerts et al. (2007c)
CA Permanent raised beds + residues Limon-Ortega et al. (2006)
CA Zero tillage + residue Mikha and Rice (2004)
CA Zero tillage + residue Roldan et al. (2007)
CA Zero tillage + residue Franzluebbers (2002)
Soil water content CA Zero tillage + residues or manure Anikwe et al. (2003)
CA Zero tillage + residue Govaerts et al. (2009b)
CA Permanent raised beds + residues Govaerts et al. (2007c)
CA Minimum till + residues + cotton/wheat Hulugalle et al. (2002)
CA = CONV. TILL. Zero tillage + residue Kennedy and Schillinger (2006)
CA Zero tillage + residue Li et al. (2007)
CA Zero tillage + residue Bescansa et al. (2006)
CA Zero tillage + residue Fabrizzi et al. (2005)
CA Zero tillage + residue Kemper and Derpsch (1981)
CA Zero tillage + residue Azooz and Arshad (1995)
CA Zero tillage + residue Johnson et al. (1984)
Infiltration CA Zero tillage + residue Govaerts et al. (2007a)
CA Permanent raised beds + residues Govaerts et al. (2007c)
CA Zero tillage + residue McGarry et al. (2000)
CA Zero tillage + residue Zhang et al. (2007)
CA Zero tillage + residue Pikul and Aase (1995)
CA Zero tillage + residue Cassel et al. (1995)
CA Zero tillage + residue Freebairn and Boughton (1985)
CA Zero tillage + residue Thierfelder et al. (2005)
CA Permanent raised beds + residues Verhulst et al. (2009)
Erosion CONV. TILL. Zero tillage + residue Cassel et al. (1995)
CONV. TILL. Zero tillage + residue Freebairn and Boughton (1985)
CONV. TILL. Zero tillage + residue Thierfelder et al. (2005)
CONV. TILL. Zero tillage + residue Kemper and Derpsch (1981)
CONV. TILL. Permanent raised beds + residue Verhulst et al. (2009)
CONV. TILL. Zero tillage + residue Zhang et al. (2007)
CONV. TILL. Zero tillage + residue Schuller et al. (2007)
CONV. TILL. Zero tillage + residue Montgomery (2007)
Earthworm CA Zero tillage + residue Kladivko (2001)
populations CA Zero tillage + residue Barnes and Ellis (1979)
CA Zero tillage + residue Gerard and Hay (1979)
Soil sodicity and CONV. TILL. Permanent raised beds + residues Govaerts et al. (2007c)
salinity CONV. TILL. Minimum tillage Hulugalle and Entwistle (1997)
CONV. TILL. Permanent raised beds + residues Sayre (2005)
CONV. TILL. = CA Zero tillage + residue Du Preez et al. (2001)
CONV. TILL. = CA Zero tillage + residue Franzluebbers and Hons (1996)
Fuel use in soil CONV. TILL. Zero tillage Erenstain et al. (2008)
preparation CONV. TILL. Zero tillage + residue West and Marland (2002)
CONV. TILL. Zero tillage + residue Wang and Dalal (2006)
CONV. TILL. Zero tillage + residue Robertson et al. (2000)
a CA, conservation agriculture; CONV. TILL., conventional tillage-based system.
186 P.R. Hobbs and B. Govaerts

(a)
300

250
Moisture content (mm)

200

150

100

50
Removal Retention
0
30 40 50 60 70 80 90 100 110 120 130
Time after planting (days)

(b)
300
Moisture content (mm)

250

200

150

Burning Full retention

100
-40 -20 0 20 40 60 80 100 120
Time after planting (days)

Fig. 10.5.  The effect of residue management on moisture content in the profile (0–60 cm) throughout the
growing season in the wheat phase of the rotation in the zero-till treatments. (a) Residue removal or
retention in the long-term rainfed sustainability trial in the highlands of Central Mexico (described in
Govaerts et al., 2005). (b) Burning of residue or residue retention in the long-term irrigated sustainability
trial in Ciudad Obregón, North Mexico (irrigations 28 days before and 43, 71 and 95 days after planting)
(adapted from Verhulst et al., 2009).

1999); zero tillage with residue retention where residue was retained and intermedi-
decreases the frequency and intensity of ate results (43%) for conventionally tilled
short mid-season droughts (Blevins et al., beds (Verhulst et al., 2009). This shows that
1971; Bradford and Peterson, 2000). Also, more than zero tillage is needed to buffer
in irrigated environments CA is a key strat- droughts; the retention of at least part of
egy to increase water-use efficiency. the crop residue is essential for success with
Preliminary results for the same long-term the zero-tillage system. The permanent soil
irrigation sustainability trial in north cover also protects the soil from erosion.
Mexico resulted in the permanent raised The key to successful CA in rainfed areas will
beds with residue burned having a very low be convincing farmers to leave some of their
average irrigation efficiency of 24% valuable crop residues on the soil surface to
compared to 52% for permanent raised beds obtain the benefits of permanent cover.
 Conservation Agriculture Buffering Climate Change 187

Drought tolerance will be increased in
some areas with CA, but resistance to flood-
ing will be key in other areas. The increased
infiltration resulting from CA in combina-
tion with the permanent raised-bed system
will help to mitigate the effects of temporary
flooding. Figure 10.6 shows how a severe
rainfall event (30 mm in approximately 1 h)
in the International Maize and Wheat
Improvement Center (CIMMYT) high rain-
fall humid (2640 m above sea level; 19.17°N,
99.33°W silty clay loam soil of volcanic
origin) experiment station in the central
highlands of Mexico results in ponding water
and a flooded crop at the lower end of the
field in the conventionally tilled field, while
in an adjacent CA field with permanent
raised beds and residue retained on the soil
surface the standing water is in the furrows,
slowly infiltrating, resulting in no standing
water at the lower end of the field.
CA will increase soil penetrability of roots
as a result of increased biological porosity
caused by undisturbed previous crop root
channels and biological activity of fungal,
mycorrhizal and faunal organisms (Table
10.1). In general, earthworm abundance,
diversity and activity have been found to
increase under CA when compared to
conventional agriculture (Kladivko, 2001;
Verhulst et al., 2010). Earthworm activity is
reported to increase soil macroporosity,
especially when populations are significant
(Shipitalo and Protz, 1988). A soil matrix
with macro-pores offers greater potential for
undisturbed root growth because the roots

(a) (b)

(c) (d)

Fig. 10.6.  The result of a severe rainfall event (30 mm in ∼1 h) in a conventionally tilled field (a and c) and
an adjacent conservation agriculture field with permanent raised beds and crop residue retained on the
soil surface (b and d) in the CIMMYT high rainfall humid (2640 m above sea level; 19.17°N, 99.33°W silty
clay loam soil of volcanic origin) experiment station in the central highlands of Mexico (photographs
courtesy of F. Delgado).
188 P.R. Hobbs and B. Govaerts
can bypass the zones of high mechanical
impedance (Lipiec and Hatano, 2003) and
increase the root zone. Changed tempera-
ture patterns and increased soil temperature
especially at seeding and seedling emergence
can negatively affect crop production. In
tropical hot soils, mulch cover reduces soil
peak temperatures that are too high for opti-
mum growth and development to an appro-
priate level, favouring biological activity,
initial crop growth and root development
during the growing season (Acharya et al.,
1998; Oliveira et al., 2001). In CA, soil-
surface-retained residue affects soil tempera-
ture through its effect on the energy balance;
tillage operations increase the rates of soil
drying and heating because tillage disturbs
the soil surface and increases the air pockets
in which evaporation occurs (Licht and
Al-Kaisi, 2005). Soil temperatures in surface
layers can be significantly lower (often
between 2 and 8°C) during daytime (in
summer) in zero-tilled soils with residue
retention compared to conventional tillage
(Oliveira et al., 2001). In these same studies,
during the night, the insulation effect of the
residues led to higher temperatures so there
was a lower amplitude of soil temperature
with zero tillage.
Soil sodicity and salinity can be ameli-
orated by CA practices (Table 10.1).
According to Govaerts et al. (2007c), perman-
ent raised-bed planting is a technology that
reduces soil sodicity under rainfed condi-
tions. They found the sodium (Na) concen-
tration to be 2.64 and 1.80 times lower in
the 0–5 cm and 5–20 cm layers, respectively,
in permanent raised beds compared to
conventionally tilled raised beds. Further­
more, the Na concentration increased with
decreasing amounts of residue retained on
the permanent raised beds. Compared to
conventional tillage, values of exchangeable
Na, exchangeable Na percentage and disper-
sion index were lower in an irrigated vertisol
after 9 years of minimum tillage (Hulugalle
and Entwistle, 1997). Also, Sayre (2005)
reported reduced sodicity and salinity in soil
under permanent raised beds with partial or
full residue retention compared to conven-
tionally tilled raised beds, which is import-
ant for saline areas. The combination of zero
tillage with sufficient crop residue retention
will reduce evaporation at the topsoil and, as
such, salt accumulation.
Reduced CO2 emissions using
conservation agriculture
In terms of CO2 emissions, CA results in a
reduction of C emissions and may also help
sequester C in the soil. Minimal soil disturb-
ance results in less exposure of the soil
organic matter to oxidation and lower CO2
emissions to the atmosphere compared to
tilled soils. As mentioned previously there
are also significant savings in diesel use and
thus lower CO2 emissions. This can be signifi-
cant as shown from data collected in the
rice–wheat systems of South Asia (Erenstein
et al., 2008). The data from their 2003/04
survey of farmers adopting zero tillage in
Haryana (India) and Punjab (Pakistan) indi-
cated an average saving of 35 l of diesel for
land preparation, or 98 kg C/ha. Farmers
averaged one pass of the tractor with zero
tillage for seeding versus eight passes for
tilled soils. The soil physical properties left
after rice cultivation are poor and it takes
multiple passes of a tined cultivator to get
what farmers feel is a suitable tilth for plant-
ing wheat. One litre of diesel contains 0.74
kg C and emits 2.67 kg CO2 (Environmental
Protection Agency, 2009). More data on
fossil fuel reduction through zero tillage can
be found in Ortiz-Monasterio et al. (Chapter
9, this volume).
There are numerous reports that show
that zero tillage, and especially zero tillage
with crop residue retention, can result in
increased soil C in the surface layers. In order
to better understand the influence of differ-
ent management practices, with special
emphasis on tillage, crop rotation and resi-
due management, on C sequestration,
Govaerts et al. (2009a) did an extensive
literature review. Some of the already exist-
ing reviews on the influence of agriculture
and management on C sequestration made
by West and Post (2002), Jarecki and Lal
(2003), VandenBygaart et al. (2003) and
Blanco-Canqui and Lal (2008) were used as a
basis and completed through a further
 Conservation Agriculture Buffering Climate Change 189
literature­ search. In seven of the 78 cases
chosen, the soil C stock was lower in zero
tillage compared to conventional tillage, in
40 cases it was higher and in 31 cases there
was no significant difference. Another review
of 67 long-term experiments that included
276 paired treatments indicated that a
change from conventional tillage to no till
can sequester 57 ± 14 g C/m2/year (West
and Post, 2002). As results do not always
point in the same direction, more research is
needed, especially in the tropical areas where
good quantitative information is lacking.
Traditionally, farmers have removed these
residues for other uses such as feeding
animals, buried them through tillage or in
high production areas have mostly burnt
them in the field. The latter releases a large
quantity of GHGs and pollutes the air. More
details on CA and its effect on C sequestra-
tion can be found in Ortiz-Monasterio et al.
(Chapter 9, this volume).
Mitigation of CH4 through conservation
agriculture
Changes in land use, especially cultivation of
formerly undisturbed soils, strongly decrease
CH4 oxidation and consequently the uptake
of atmospheric CH4 by the soil (Hütsch,
1998; Chan and Parkin, 2001). Typically,
agricultural soils vary from being minor
emitters of CH4 to small sinks for atmos-
pheric CH4 (Chan and Parkin, 2001). Hütsch
(1998) suggested that a reduction in tillage
intensity could help minimize the adverse
effects of cultivation on soil CH4 uptake. But
according to Omonode et al. (2007), anaer-
obic conditions are frequent under zero till-
age and consequently there will be an
emission of CH4. As there are a limited
number of studies, the impact of tillage on
the CH4 flux in a crop production system is
still unclear (Jacinthe and Lal, 2004).
A major contributor to CH4 emissions
from agricultural production is the produc-
tion of rice. About 90% of rice land is, at
least temporarily, flooded. The magnitude
and pattern of CH4 emissions from rice fields
are mainly determined by water regime and
organic inputs. Flooding of the soil is a
prerequisite for sustained emissions of CH4
(Ortiz-Monasterio et al., Chapter 9, this
volume). Reduction in CH4 emissions from
agriculture can, therefore, to a large extent
be accomplished by growing rice aerobically,
rather than flooded and anaerobic as is pres-
ently practised in large areas of rice produ-
cing countries. This can be done by wetting
and drying, planting rice on beds, increasing
water percolation through the soil profile,
and changing from anaerobic rice to aerobic
rice. In line with this, more recent recom-
mendations for irrigated rice indicate that
continuous flooding is not needed, but
instead irrigation water should be applied
after the soils have dried to where fine cracks
appear (Ortiz-Monasterio et al., Chapter 9,
this volume). This not only reduces the
amount of water used but also reduces CH4
emissions. In rainfed lowland systems less
CH4 would be emitted than in irrigated
systems because of natural wetting and
drying cycles caused by intermittent rain,
unless the fields remain flooded for longer
periods, such as in deepwater rice systems.
An added benefit of CA-grown rice would be
substantially reduced water costs (Castaneda
et al., 2004). However, major efforts in
research and development have to be made
to develop the optimal CA and aerobic rice
production package, as years of research
including crop variety development and
breeding have focused on flooded rice
systems.
Changing farmer practices from flooded
to aerobic rice is not easy because farmers
prefer to grow lowland rice the traditional
way: transplanting seedlings into soils that
have been puddled (ploughed wet), a process
that promotes ponding of water and anaer-
obic conditions. The standing water makes it
easier for weed control and also makes nutri-
ents more available since anaerobic soils
equilibrate closer to a pH of 7.0 where essen-
tial nutrients are more available. Also, in
some lowland areas rice may be the only crop
that can be grown because of natural flood-
ing, rice being one of the few crops that are
adapted to anaerobic and flooded condi-
tions. Experiments by the International Rice
Research Institute (IRRI) in the Philippines
demonstrate the large reductions in water
190 P.R. Hobbs and B. Govaerts
use by aerobic compared to flooded rice.
These experiments were conducted in the
wet and dry seasons over 2 years and
concluded that aerobic rice used 73% less
water for land preparation and 56% less
during the cropping season compared to the
flooded fields (Castaneda et al., 2004).
Aerobic rice also used the rainfall more effec-
tively during the wet season. However, the
savings in water came at the expense of a
loss in yield: 28% in the dry season and 20%
in the wet season. What was not clear was
whether the varieties selected for the experi-
ment were upland or lowland varieties. Note
that both the aerobic and flooded plots had
transplanted rice with the soils flooded for
several days in the aerobic plots and puddled
in the flooded plots. The authors concluded
that there was a need to breed varieties
better adapted to aerobic conditions.
The yield reduction in aerobic rice
compared to flooded rice has been reported
by other researchers. In some Chinese
experiments, yields of aerobic rice were
11–31% lower than under flooded condi-
tions with the authors suggesting lower
moisture during tillering and deficiency of N
and microelements as prime causes (Dittert
et al., 2002), although water use was up to
60% less with aerobic rice in some sites.
Other data from rice–wheat areas in South
Asia show savings in water but lower aerobic
compared to flooded rice yields on bed-
planted rice (Sharma et al., 2002); iron and
zinc deficiencies were present in the aerobic
plots. In other studies in rice–wheat areas of
South Asia, weeds, nematodes (Meloidogyne
sp.) and iron deficiency appeared to lower
yields on flat and bed-planted aerobic rice
(Singh et al., 2002). However, both these
rice–wheat experiments were done on plots
where weed densities were higher than in
farmers’ fields. Data from Eastern Uttar
Pradesh in India collected from many farm-
ers’ field experiments averaged over 3 years
(2005–2007) showed better production
under both flat (Singh et al., 2009b) and bed-
planted systems (Singh et al., 2009a) for the
aerobic, direct seeded and zero-till rice treat-
ments compared to the traditional flooded
systems. The direct-seeded and zero-till
treatments used less water, reduced costs,
used more herbicide but had greater yields
(average of 0.5 t/ha) and greater net
returns.
CA applied to rice could be a way to reduce
CH4 emissions since it would eliminate the
puddling and encourage more percolation of
water through the soil profile and help aerate
the soil. The effect would be larger in bed-
planted rice since aeration would be greater.
Obviously, farmers will not accept large
reductions in rice yields so much more
research and development is needed to
develop the correct management systems
for CA on different soils and under different
water regimes; these include development of
better varieties, weed control strategies,
nutrient applications, seeding equipment
and more.
Mitigation of N2O emissions through
conservation agriculture
The two main processes of the N cycle that
determine the production of N2O are nitrifi-
cation and denitrification. Denitrification
occurs under anaerobic conditions where
nitrate is reduced to various N forms as
follows:
NO3–  NO  NO  N O N
2
–
2 2
Any management practice that creates
anaerobic conditions including flooding,
especially in heavy textured soils, when
nitrate is present will lead to increased N2O
emissions (Ball et al., 1999). These emissions
can be reduced by aerating the soil, espe-
cially in coarse textured soils, as evidenced
by reduced emissions in permanent raised-
bed planted crops (Patiño-Zúñiga et al.,
2009).
The other N cycle process that generates
N2O is nitrification. This occurs under
aerobic conditions with the oxidation of
ammonia to NO2– and finally NO3–. If this
soil is then flooded, denitrification can occur.
N2O is also released from soils to the atmos-
phere during nitrification of ammonium and
ammonium-producing fertilizers under
aerobic conditions. This can be significant
during fertilizer applications. Such emis-
sions can be greatly reduced through the use
 Conservation Agriculture Buffering Climate Change 191
of nitrapyrin, which inhibits nitrification of
ammonium by soil microorganisms.
These two N-cycle processes are mainly
influenced by factors such as soil tempera-
ture, soil moisture content, pH, supply of C
and N compounds (Skiba et al., 1998; Lee et
al., 2006) and soil electrical conductivity
(Adviento-Borbe et al., 2006). These factors
can be manipulated by tillage (Venterea et
al., 2005), residue management, irrigation
(Qian et al., 1997) and the application of N
fertilizer (Smith et al., 1997). Increased soil
organic matter can also result in increased
N2O emission through the increase in N
cycling in the soil as nitrification is stimu-
lated (Butterbach-Bahl et al., 2004). However,
zero tillage combined with residue retention
results in a better soil structure, facilitating
O2 diffusion and reducing the amount of
anaerobic sites in the soil, and stimulating
oxidation of CH4, but it remains to be seen
how emissions of NO and N2O are really
affected.
GHG emissions were studied in water-
saving experiments with rice in China
(Dittert et al., 2002). The results showed a
significant drop in CH4 emissions with a
more aerobic rice production system
compared to a flooded rice system, but N2O
emissions increased, especially after N fertil-
izer application. The researchers concluded
that N fertilizer applications needed to be
optimized to minimize N2O emissions, espe-
cially since this gas has a much greater heat-
ing potential than CH4 or CO2. Patiño-Zúñiga
et al. (2009) observed in a laboratory incuba-
tion experiment that the N2O emission from
conventional tillage with residue retention
was 2.3 times larger compared to no tillage
with residue retention. Jacinthe and Dick
(1997) observed that the seasonal N2O emis-
sion from zero tillage was significantly lower
than from conventional tillage (chisel till-
age) under continuous maize, maize–
soybean rotation and maize–soybean/
wheat–hairy vetch rotation in Ohio, USA.
Kessavalou et al. (1998) demonstrated that
the application of tillage during fallow
increased the N2O flux by almost 100% rela-
tive to the no-tillage treatment. Robertson
et al. (2000) reported that N2O emissions
from zero tillage were similar to or slightly
higher than from conventional tillage under
maize–wheat–soybean rotations in the
Midwest USA. Rochette et al. (2008) demon-
strated in a 3-year study in East Canada that
the average N2O emissions from zero tillage
were more than double those from conven-
tional tillage in a heavy clay soil. In a loam
soil, the average emissions during the 3 years
were similar in the two treatments. Rochette
(2008) concluded that N2O emissions only
increased in poorly drained, finely textured
agricultural soils under zero tillage located
in regions with a humid climate, but not in
well-drained aerated soils. Six et al. (2004)
compiled all available data of soil-derived
GHG emission comparisons between
conventional tilled and no-tillage systems
for humid and dry temperate climates. They
concluded that in both humid and dry
climates, differences in N2O emissions
between the two tillage systems changed
over time. In the first 10 years, N2O fluxes
were higher in zero tillage compared to
conventional tillage, regardless of climate.
After 20 years, however, N2O emissions in
humid climates were lower in zero tillage
than conventional tillage and were similar
between tillage systems in the dry climate.
The key for the implementation of CA as
a GHG mitigation strategy is the under-
standing of the integrated effect of the prac-
tice on all GHGs and developing the
necessary component technologies and
fertilization practices to reduce the emis-
sions of N2O, since any gains in reduction of
CO2 and CH4 emissions could be lost if these
practices resulted in increased N2O emis-
sions. Part of the conflicting results with
zero-tillage and CA practices is related to
development of the optimal implementation
of the system. Years of research and develop-
ment have been spent to optimize conven-
tional tillage systems but a knowledge base
for CA on all production-related components
in different locations has yet to be devel-
oped. For example land levelling is a compo-
nent technology that drastically increases
the efficiency of zero tillage and CA in flood
irrigated systems. In this case farmers level
their fields using equipment on their farms.
However, the use of laser land levelling
results in an even better field level.
192 P.R. Hobbs and B. Govaerts
Well-levelled fields give much better results
with CA whether they are planted on the flat
or on beds; in particular, water productivity
can be significantly improved.
Accelerating the adoption of conservation
agriculture
CA adoption statistics are hard to quantify,
since statistics are not collected on this
specific management practice. Instead, the
acreage of zero tillage is used as a proxy for
CA. This tends to overestimate the area since
many farmers do not adopt all three prin-
ciples of CA. For example farmers in South
Asia will adopt zero tillage for wheat planted
after rice, but the rice crop is still planted
with full tillage and puddling of soils (Hobbs
et al., 2005). In dryland areas with low
biomass yields and competing uses for crop
residues, farmers may not be able to spare
needed amounts of residues for optimal CA
management. The latest statistics on adop-
tion of zero tillage worldwide is 105 million
ha (Derpsch and Friedrich, 2009). Although
this is only 7.5% of the 1.4 billion ha of total
arable land (FAO, 2003) it does provide
benefits in terms of reducing GHG emissions
and does provide the potential for mitigat-
ing global climate change if adoption is
increased.
There are several factors that need to be
addressed to accelerate the adoption of CA.
Probably the most important factor in adop-
tion of CA is overcoming the bias or mindset
about tillage. Changing the mindset of farm-
ers from a system that has promoted tillage
for centuries to one where tillage is reduced
or even avoided is a major obstacle to adop-
tion. There are many examples of where
farmers were ridiculed by their neighbours
when they first tried this technology. In
some cases, farmers actually ploughed up
their fields rather than be subjected to this
criticism. But once the crop emerged and the
farmer and his or her neighbours could see
that tillage was not necessary for a good
plant stand they gained confidence and in
fact became the best extension agents for
this technology. The next step after identify-
ing a willing farmer was to expose other
farmers to the performance of CA in the
field. This was done by word-of-mouth from
farmer to farmer but also by visits of farm-
ers from other villages and discussion with
the innovative farmer and what he or she
had done. Once farmers were convinced that
they could grow a successful crop without
tillage they began to think of the many other
benefits that CA would give them.
Another critical factor for adoption of CA
is the availability of suitable equipment to
enable farmers to successfully plant their
crops without tillage. This is a factor for any
new technology; the adoption of conserva-
tion tillage following the dust bowl of the
1930s was dependent on the development
of seed drills that could plant into soil with
minimum tillage and with loose residue on
the surface. This led to the development of
disk-based seed drills that could cut the resi-
due and place the seed in the soil at the
correct depth for good germination. Today
there is a whole array of different equipment
for planting into minimally disturbed soil.
These drills also place fertilizer in the soil at
the time of planting which improves the effi-
ciency of nutrient application. This equip-
ment is efficient at planting seed and getting
good plant stands; however, these expensive
and power-thirsty zero-tillage drills are not
well adapted to some developing countries
with smaller powered tractors and in some
cases no tractors at all. In these cases,
researchers and engineers have developed
equipment that is lower in cost, lighter and
can be powered by smaller tractors. There is
also manual and animal-powered equipment
that can be used to plant seed into any zero-
tillage field. Once the equipment is made
available to farmers for experimentation,
they see for themselves the benefits of
reduced costs and time, improved produc-
tion and improved soil health. However, it is
clear that in order to spread the CA technol-
ogy a dynamic of innovation of equipment
has to be catalysed with close interaction
between farmer, technician, machine build-
ers, local private enterprises, craftsman,
scientists, engineers, etc.
CA can be scale neutral. The key is to find
mechanisms that allow even resource-poor
farmers to practise and experiment with this
 Conservation Agriculture Buffering Climate Change 193
technology, making sure they have access to
the equipment and also the knowledge about
the benefits. In some cases in developing
countries farmers do not own tractors.
Gaining access to equipment, however, can
be found through service providers. A farmer
who owns a tractor and has purchased CA
equipment provides a service to his poorer
neighbour on rent. The resource-poor farmer
can benefit from the technology by getting
his or her fields planted on time and with
the minimal amount of time, leaving the
farmer to find other productive employ-
ment. In this way he or she gets better yields
at less cost and time, leading to better
returns from agriculture. If training is
imparted to the service provider then the
quality of planting is also maintained. The
service provider can also be linked to local
manufacturers so that the farmer can get a
good supply of spare parts but also provide
feedback to the manufacturer about ways to
improve the efficiency of the equipment. In
fact, farmers who did not own tractors were
able to plough their fields by the same rental
service system prior to the introduction of
zero tillage.
The old linear top-down approach to
extension is not very efficient in the case of
CA. Farmers have to see for themselves and
overcome their apprehensions before they
are willing to adopt this new technology. In
this case it is important that equipment is
made available to farmers, that they are
trained in its proper use and that the equip-
ment is left with the farmers to experiment
on their own farm. If scientists or extension
agents only conduct demonstrations in farm-
ers’ fields and then take the equipment back
to their experiment stations, adoption rates
are much lower. An example of this can be
found in India where in the state of Haryana,
farmers were given the seed drills and
sufficient training and left to experiment.
Adoption rates were very rapid (Malik et al.,
2002). In Punjab and Uttar Pradesh states in
India, researchers and extension agents used
the equipment for demonstrations and then
carried the equipment back to their stations.
In this case adoption was very slow.
A network of stakeholders has to be
developed in order to address various issues
that arise during adoption. Researchers and
extension agents need to interact with farm-
ers to address issues and problems that arise
during the initial phases of CA adoption.
Local manufacturers need to be actively
involved with farmers to identify improve-
ments to machinery that lead to better
performance. Banks and credit agencies are
needed to provide funds for farmers to buy
equipment. Input agencies are needed to
supply fertilizers and other inputs needed
for good yields. These can be coordinated
through public institutions or through
public–private collaborations. However, it is
clear that rather than a linear line of adop-
tion an inter-actor innovation process has to
be promoted. Therefore, a network of decen-
tralized learning hubs within different farm-
ing systems and agroecological zones should
be developed (Sayre and Govaerts, 2009). In
those hubs, an intense contact and exchange
of information is organized between the
different partners in the research and exten-
sion process. Multiple actors within the
production system (farmers, scientists,
machine builders, decision makers, input
suppliers, etc.) come together in the hubs,
work together and learn together in order to
multiply this effort in an intense extension
and out-scaling process. Because of the
multifaceted nature of CA technology devel-
opment and extension, activities should be
concentrated in a few defined locations
representative of certain farming systems
rather than having lower intensity efforts on
a wide scale. Through the research and train-
ing, regional CA networks are established to
facilitate and foment research and the exten-
sion of innovation systems and technolo-
gies. Research at the hubs also provides an
example of the functionality of CA systems,
helping to break down the culture of the
plough. The hubs are linked to the strategic
science platforms operated by international
centres and national research institutes to
synthesize a global understanding of CA and
its adaptability to different environments,
cropping systems and farmers’ circum-
stances. Innovative farmers are intensively
involved and are the key factor for the build-
up and extension of a successful CA network
that leads to a sustainable impact.
194 P.R. Hobbs and B. Govaerts
Conclusions
Global climate change caused by anthropo-
genic GHG emissions is already affecting
weather patterns including temperatures
and rainfall. CA that consists of minimal soil
disturbance, permanent ground cover and
crop rotations is a management system that
can alleviate some of the effects of climate
change. CA results in healthier soils, both
physically and biologically, and this in turn
improves nutrient cycling and crop growth.
Water infiltration and soil penetration by
roots is increased allowing crops to better
adapt to lower rainfall and make better use
of irrigation water. Water and wind erosion
is also reduced by CA since the soil surface is
protected from erosion and water runoff is
lowered as more water enters the soil profile.
CA creates soils and production systems
more resilient to climate variation and risk.
Agricultural production is one contributor
to GHG emissions including CO2, CH4 and
N2O, the three main gases influencing global
warming. In fact, agriculture is a major
contributor to CH4 and N2O emissions, two
gases with greater warming potential than
CO2, although emitted at lower concentra-
tions. CA can mitigate these GHG emissions.
CH4 is a by-product of rice cultivation under
flooded conditions. Growing rice with less
water and adopting CA practices can reduce
CH4 emissions. However, care has to be
taken with fertilizer management to mini-
mize N2O emissions that can increase under
the resulting aerobic conditions. CA can also
substantially reduce CO2 emissions through
reduced diesel use and potentially increase
the sequestration of C in the soil. Therefore,
CA not only helps crops adjust to changes in
climate but also helps reduce GHG emis-
sions. At present just over 105 million ha of
land worldwide uses zero tillage in agricul-
ture. Not all of it is CA but it still impacts
positively in the global climate change
scenario. In order for this acreage to increase
attempts are needed to expand adoption
through better extension systems, farmer
knowledge and making suitable equipment
available to farmers. Much more integrated
research and development is needed to
develop the fundamental knowledge base
for CA as well as to fine tune CA to specific
locations and identify suitable germplasm,
fertility management, weed control and
control of other biotic factors to move this
technology onwards. Because of the multi-
faceted nature of CA technology develop-
ment and extension, activities should be
concentrated in a few defined locations
representative of specific farming systems
rather than having lower intensity efforts on
a wide scale. Scaling up can then occur from
these hubs or focal points by using the farm-
ers and fields as demonstrations to other
farmers in surrounding areas.
Acknowledgements
The authors wish to thank Nele Verhulst and
Adrian Carrillo Garcia for their valuable help
with this chapter.
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92, 122–128.
11
Management of Resident Soil
Microbial Community Structure
and Function to Suppress
Soilborne Disease Development

Mark Mazzola

Abstract
Climate change is likely to alter the distribution and severity of soilborne diseases affecting both
intensive and low-input agricultural production systems. Naturally occurring disease suppressive soils
have been documented in a variety of cropping systems, and in many instances the biological attributes
contributing to suppressiveness have been identified. While these studies have often yielded an
understanding of operative mechanisms leading to the suppressive state, significant difficulty has
been realized in the transfer of this knowledge into the development of effective field-level disease
control practices. Early efforts focused on the inundative application of individual or mixtures of
microbial strains recovered from these systems, and known to function in specific soil suppressiveness.
However, the introduction of biological agents into non-native soil ecosystems typically fails to yield
commercially viable or consistent levels of disease control. Of late, greater emphasis has been placed
on manipulation of the cropping system to manage resident beneficial rhizosphere microorganisms as
a means to suppress soilborne plant pathogens. One such strategy is the cropping of specific plant
species or genotypes, or the application of soil amendments with the goal of selectively enhancing
disease suppressive microbial communities. This chapter will briefly review the existence of biologically
functional disease suppressive soils, document the research history supporting the potential in
managing microbial communities for disease control, describe methods available for the effective
manipulation of bioactive populations, and describe specific examples demonstrating the effective
application of the approach.

Introduction year worldwide (Bird and Kaloshian, 2003),

Soilborne diseases present significant
constraints to continued utilization of arable
land in both intensive and low-input agricul-
tural production systems. Diseases incited
by fungi and bacteria were reported to
account for yield losses ranging on average
from 7 to 15% during the period 2001–2003
for the major world crops (Oerke, 2005).
Among the 2000 major plant diseases affect-
ing the principle crops produced in the USA,
approximately 90% are caused by soilborne
pathogens (Lewis and Papavizas, 1991).
Economic losses due to plant parasitic nema-
todes have been estimated at US$100 billion/
while in the USA soilborne diseases are esti-
mated to produce crop losses that exceed
US$4 billion/year (Lumsden et al., 1995).
Relative to those employed against diseases
affecting aerial surfaces of plants (see
Legrève and Duveiller, Chapter 4, this
volume), methods for the management of
soilborne diseases tend to yield less compre-
hensive disease control and there are few
effective disease control options applicable
in a post-plant or perennial crop production
setting. Certain practices currently employed
for the control of soilborne diseases can
confer significant impact on society and the
environment that far exceeds the direct

200 © CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds)
 Soil Microbial Community Management 201

costs to the grower and consumers. For
example, in the case of soil fumigation,
although effective disease control may be
achieved, such a practice results in major
ecological disturbances to the production
system as a whole. In the instance of certain
chemicals such as methyl bromide, a fumi-
gant once widely used for the control of soil-
borne plant pathogens, disease control
activities not only directly impact the treated
biological system but can also adversely
impact air quality and may contribute
broadly to environmental degradation.
Disease management strategies that are
considered to impart a more ecologically
sustainable footprint, such as host resist-
ance or the application of microbial
biological control agents, are generally effec-
tive towards a more limited and targeted
pathogen population than chemical control
alternatives (Table 11.1). With few excep-
tions, biological controls have not attained
the level of performance in terms of both
efficacy and consistency required to achieve
widespread adoption for use in commercial
field-level agricultural production systems.
Host resistance is a proven and effective
strategy for the management of numerous
economically important foliar plant diseases
such as those incited by biotrophic rust fungi
(McIntosh et al., 1995). Fewer examples
exist for soilborne pathogens or parasites,
however effective host resistance has been
obtained for the control of particular agents
such as the ubiquitous and specialized
fungus Fusarium oxysporum (El Mohtar et al.,
2007; Herman and Perl-Treves, 2007).
Likewise, a multitude of resistance sources
in cereals to the cereal cyst nematode have
been documented with resistance conferred
by a single host gene (Nicol and Rivoal,
2008). Climate change will be likely to have
significant impacts on both of these disease
control options, which may further limit
their potential for the management of soil-
borne plant diseases. A dominant impedi-
ment to the broad-scale effective use of
microbial biological control agents is their
failure to persist at required threshold popu-
lations in non-native or environmentally
extreme environments. Thus, several micro-
bial groups currently viewed as an effective
source of biological control agents (e.g.
Pseudomonas spp.) may exhibit impaired
performance under the predicted climate
change models. Likewise, temperature and
drought stress associated with climate
change has the potential to modulate the
effectiveness of host gene resistance, and
not necessarily in a predictable fashion
(Garrett et al., 2006).
As climate is undergoing a period of rapid
change, the underlying functional biology
indigenous to any ecosystem will itself
undergo transformations allowing for adap-
tation of the resident biology to the altered
environment (Jarvis et al., Chapter 2; Legrève
and Duveiller, Chapter 4, this volume). In

Table 11.1.  Successful non-chemical approaches for control of soilborne diseases.

Method References
Host resistance Fazio et al. (2006), El Mohtar et al. (2007), Herman and
Perl-Treves (2007), Nicol and Rivoal (2008)
Soil solarization Katan (1987)
Crop rotation Larkin and Honeycutt (2006), Subbarao et al. (2007), Kirkegaard
et al. (2008)
Tillage Cook et al. (1990), Roget et al. (1996)
Biological control Kerr (1980), Fravel (2005)
Disease suppressive soils (native) Stotzky and Martin (1963), Rouxel et al. (1979)
Disease suppressive soils induced
via:
  Plant residue amendments Cohen et al. (2005), Wiggins and Kinkel (2005a)
  Tillage Peters et al. (2003)
  Cropping sequence Shipton et al. (1973)
Specific plant genotype Larkin et al. (1993), Mazzola and Gu (2002), Mazzola et al.
(2004)
202 M. Mazzola
some instances this will yield changes in
distribution or incidence of specific plant
pests, with parasites of previously restricted
distribution perhaps becoming more cosmo-
politan. Nevertheless, within the context of
this biological community many elements
exist that function to enhance plant growth,
development and survival. These include
such entities as natural enemies, many of
which have been effectively utilized in pest
management systems for the biological
control of plant parasitic insects. The utiliza-
tion of natural enemies often relies upon the
inundative release of one or a few native or
non-native predators or parasitoids, a model
commonly employed in the application of
microbial biological control (Myers et al.,
1989). Within the entomological discipline,
an alternative model has been utilized at
times to promote native biological control.
Such a strategy relies upon the establishment
of systems designed to enhance the abun-
dance and diversity of naturally occurring
insect predators, ranging from insectivorous
birds to the more commonly considered
insect predators. Such systems may involve
the establishment of mixed cropping systems,
internal or external refugia which provide
habitats for beneficial organisms to enable
pesticide avoidance, an alternative food
source or appropriate habitat needs external
to the crop production season (Bianchi et al.,
2006).
Within the context of soilborne plant
disease management, attempts to employ
microbial biological control have typically
involved the inundative release of non-
native microorganisms into soil systems.
Such an approach assumes that the intro-
duced microbial agent or mixture will effec-
tively compete with the resident microbial
community, efficiently colonize the rhizo-
sphere of the targeted plant and persist in
the rhizosphere at the threshold population
required for activity during the period of
plant susceptibility, and also that the active
mechanism is operative in the environment
into which it has been applied. Soil dwelling
microbial antagonists of plant pests and
pathogens have been studied extensively as
to their role in the development of soil
suppressiveness (Weller et al., 2002). These
same entities have served as a primary
source of microorganisms that have subse-
quently been evaluated for their capacity to
function as agents for the biological control
of soilborne plant diseases. Despite the
extensive study of these microbial biocon-
trol agents, there continue to exist extensive
gaps in our knowledge of the factors that
influence microbial survival and the
attributes of the system that will modulate
expression of mechanisms directly contrib-
uting to disease suppression. As such, in
general, attempts to utilize biological control
for the suppression of soilborne plant
diseases in commercial field-level produc-
tion systems have failed to yield the predicted
disease control potential of these microbial
resources. Perhaps this outcome should have
been expected as the persistence and activ-
ity of any organism in an alien environment,
while in competition with the myriad of
organisms adapted to that same soil, is
rather improbable. In addition, the func-
tional biotic milieu responsible for disease
suppression may involve a complexity of
interactions well beyond a single microbe or
microbial mixture, and may not necessarily
function outside its native abiotic matrix.
Suppressive Soils
A significant body of research has focused on
the description and function of soils possess-
ing the capacity to suppress soilborne plant
diseases. Disease suppressive soils have been
defined as those in which disease develop-
ment is minimal even in the presence of a
virulent pathogen and a susceptible host.
The concept of disease suppressive soil has
been described in terms of both general
suppression and specific suppression. Every
natural soil possesses some ability to suppress
the activity of plant pathogens due to the
presence and activity of its complement of
resident soil microorganisms (Cook and
Baker, 1983). This can readily be observed
when one compares disease progression and
severity after artificial introduction of a plant
pathogen into a natural soil relative to that
achieved in the same soil that has been
pasteurized prior to pathogen introduction.
 Soil Microbial Community Management 203
The phenomenon is termed general suppres-
sion and is thought to be directly related to
the total amount of microbial activity in a
given soil rather than operating through the
action of a specific microorganism or specific
group of microorganisms.
While general suppression is a compo-
nent of disease suppressive soils, manipula-
tion or exploitation of the biological
components contributing to the phenom-
enon termed specific suppression has
perhaps more commonly been the desire of
researchers and crop producers when formu-
lating a disease management strategy.
Certain disease suppressive soils are natur-
ally occurring and suppressiveness is attrib-
uted in part to physical or chemical attributes
of the soil (Stotzky and Martin, 1963; Stutz
et al., 1989), or may be modulated by such
properties (Amir and Alabouvette, 1993). In
other systems it is accepted that suppres-
siveness is fundamentally a function of
microbiological activity resident to a given
soil. The microbial contribution to disease
suppression is confirmed by demonstrating
that the disease suppressive factor can be
transferred to a conducive soil through the
introduction of very small amounts of the
suppressive soil. Likewise, the observation
that the suppressive factor could be elimi-
nated through soil pasteurization affirmed
the role of soil microorganisms in disease
suppression. The attributes of biologically
mediated disease suppression are diverse
and the specific qualities or components of
the functional biology differ widely with the
disease of interest. For example, elevated
bacterial population diversity has been asso-
ciated with a higher degree of soil suppres-
siveness towards the fungal pathogen
Fusarium graminearum, and selective attenu-
ation of this diversity resulted in a reduction
in soil fungistasis (Wu et al., 2008). However,
in many instances specific disease suppres-
sion is attributed to the activity of an indi-
vidual or select group of microorganisms
that are antagonistic towards the target
pathogen (Weller et al., 2002). Those
instances in which soils derive disease
suppressive potential through a biologically
mediated process will be the focus of this
discussion.
Functional Biology of Disease
Suppressive Soils
Disease suppressive soils have been identi-
fied for a number of plant pathogens, with a
few of the more prominent examples includ-
ing those soils suppressive to Fusarium wilt
(Rouxel et al., 1979; Scher and Baker, 1980),
potato scab (Menzies, 1959), cyst nematode
(Westphal and Becker, 1999), Rhizoctonia
root rot (Henis et al., 1979; Barnett et al.,
2006; Garbeva et al., 2006), Pythium root
rot (Adiobo et al., 2007) and take-all of wheat
(Cook and Rovira, 1976). Harnessing the
potential of these soils as a practical means
to manage diseases in agroecosystems has
long been a goal; however, there have been
limited attempts to actively manage these
resources in the context of an overall plant
production system.
Clearly, the effective implementation of
strategies to manage resident soil microbial
communities for the suppression of soilborne
plant pathogens requires the capacity to
initially identify the biological components
involved in disease suppression. As noted
above, the biotic factors that contribute to
specific soil suppressiveness have been eluci-
dated for a number of plant-pathogen systems
(Weller et al., 2002). In certain systems, the
capacity of a soil to limit disease is elevated
over time in response to the application of
specific plant management systems. One of
the more notable examples has been docu-
mented in soils that are suppressive to the
disease take-all of wheat which is incited by
the fungal pathogen Gaeumannomyces
graminis var. tritici. In systems where wheat is
grown under continuous monoculture,
disease incidence commonly increases during
the initial few years of production but at some
point thereafter a spontaneous decline in
disease severity is realized, termed take-all
decline, and the soil remains suppressive to
the disease as long as wheat monoculture is
not interrupted (Gerlagh, 1968; Shipton et
al., 1973). Take-all decline has been observed
across geographic regions, and in multiple
instances 2,4-diacetylphloroglucinol (2,4-
DAPG)-producing fluorescent pseudomonads
have been shown to play a prominent role in
the development of take-all suppressive soils
204 M. Mazzola
(Weller et al., 2002; de Souza et al., 2003).
Fusarium wilt suppressive soils may also
develop in response to crop cultivation
(Larkin et al., 1993), and non-pathogenic
Fusarium spp. have repeatedly been impli-
cated as a factor functioning in disease
suppression (Alabouvette et al., 1996), at
times in concert with resident siderophore or
phenazine-producing fluorescent Pseudo­
monas spp. (Duijff et al., 1999; Mazurier et al.,
2009). The commonality of functional biol-
ogy and inducing agronomic practices leading
to specific suppression of a disease across
geographic regions supports the premise that
managing these phenomena is a credible
strategy to pursue for soilborne disease
management.
Management of Biologically Mediated
Soil Suppressiveness
Various attributes of a cropping system
including plant species (Garbeva et al.,
2006), input system (organic versus conven-
tional) (Workneh et al., 1993; van Bruggen,
1995; Liu et al., 2007), tillage (Peters et al.,
2003) and fertilization (Smiley, 1978),
among others, will influence ecological
processes that determine microbial commu-
nity structure and function, including its
capacity to induce suppression of soilborne
plant pathogens. These observations imply
that, given knowledge of the operative
biological mechanisms, there exists the abil-
ity to enhance or diminish the suppressive
nature of a resident microbial community
through timely application of the appropri-
ate agronomic practices (Workneh and van
Bruggen, 1994; Hoeper and Alabouvette,
1996; Pankhurst et al., 2002). As the induc-
tion of soil suppressiveness is often medi-
ated through transformations in soil
microbial communities over time (Liu and
Baker, 1980; Larkin et al., 1993; Raaijmakers
et al., 1997; Mazzola and Gu, 2002; Weller et
al., 2002), there may be a significant oppor-
tunity to manage the phenomenon, and
perhaps accelerate the onset of the disease-
suppressive state, a notable prerequisite to
the economic viability and adoption of such
a disease control strategy.
In the management of soil suppressive-
ness, it may be argued that enhancement of
overall general suppression would be the
easier course to pursue as this can be achieved
simply through elevation of general micro-
bial activity in a soil. In certain instances
such a tactic may be a viable means to achieve
disease suppression. However, as is true for
all but the most drastic control methods (e.g.
soil fumigation), it is unlikely to be a univer-
sal solution to the management of soilborne
diseases. For example, the general suppres-
sion phenomenon is reported to function in
certain soils suppressive to Pythium root rot
(Adiobo et al., 2007). In addition, control of
diseases incited by Pythium spp. in response
to addition of organic residues to soils is
often attributed to and dependent upon an
overall elevation in general soil microbial
activity (Hoitink and Boehm, 1999). While
the level of disease control attained will be
dependent upon substrate composition and
state at the time of soil incorporation
(Mandelbaum and Hadar, 1990), pursuing
this strategy for control of diseases incited
by Pythium would appear to possess signifi-
cant potential. In contrast, suppression of
other soilborne diseases, such as Rhizoctonia
root rot (Henis et al., 1979; Mazzola and Gu,
2002), may function through ‘specific
suppression’ and rely upon the activity of a
defined subset of the total soil microbial
community. Substrate-induced generation of
soil suppressiveness to Rhizoctonia root rot
was dependent upon specific microorganisms
or communities resident in the organic
substrate (Kuter et al., 1983; Kwok et al.,
1987) or the capacity of the amendment to
selectively amplify the functional popula-
tions resident to the soil (Cohen et al., 2005;
Wiggins and Kinkel, 2005a). Thus, in patho-
systems where specific suppression is the
primary determinant of disease control, even
where overall enhancement of microbial
activity realized in response to a manage-
ment practice, in the absence of the specific
functional microbial population disease
control may not be realized (Aryantha et al.,
2000; Cohen et al., 2005).
Efforts to direct development of specific
soil suppressiveness as a management tool
requires knowledge of the biological
 Soil Microbial Community Management 205
consortia­ conferring disease suppression as
well as an understanding of how any partic-
ular strategy will influence the activity of the
functional population. Many biologically
based ‘alternative’ practices have failed to
live up to their potential owing to an inabil-
ity to identify the functional population(s)
leading to pest suppression. When such
information is available, functional groups
can be monitored enabling the prediction of
pest control efficacy. For instance, the
natural development of soils suppressive
towards take-all of wheat in response to
wheat monoculture was shown to be depend-
ent upon native 2,4-DAPG-producing fluor-
escent pseudomonads attaining a threshold
population of 105 colony forming units
(cfu)/g root or greater in order to achieve
effective disease control (Raaijmakers and
Weller, 1998; de Souza et al., 2003). This
functional population can now serve as a
biological indicator to predict the efficacy of
practices (e.g. continuous wheat monocul-
ture) that lead to take-all suppressive soils.
Within the scope of a ‘functional micro-
bial population’ exists an extraordinary level
of complexity that may not be apparent nor
routinely considered in the application of
such a disease management strategy.
For instance, populations of 2,4-DAPG-
producing fluorescent pseudomonads are
genetically diverse and differ in capacity to
suppress take-all of wheat (Raaijmakers and
Weller, 2001). Wheat cultivars also differ in
both relative density and genetic compos-
ition of the 2,4-DAPG population selected
from indigenous soil populations of these
bacteria (Mazzola et al., 2004). The capacity
of the plant host to seize the benefit from a
particular functional group, and diversity in
susceptibility of the universal pathogen
population to the mode(s) of action contrib-
uting to disease suppression will also influ-
ence disease development. For instance, a
particular plant growth promoting rhizo-
bacteria that elicits defence responses in one
plant species (Tran et al., 2007) may yield no
such response in a different plant species
(Mazzola et al., 2007b). Although cyclic
lipopeptide-producing rhizobacteria func-
tion to provide control of diseases incited by
certain Pythium spp. through the zoosporo-
cidal activity of these metabolites (de Souza
et al., 2003), this mechanism obviously will
not contribute to suppression of diseases
incited by Pythium spp. for which zoospore
production is not a functional or important
component of the disease cycle (Mazzola et
al., 2007b). Thus, various attributes of an
agricultural ecosystem are likely to modulate
the development and efficacy of a disease
suppressive soil.
Strategies to Induce Specific Soil
Suppressiveness
Organic residue amendment-induced
biological soil suppressiveness
A diversity of soil amendments has been
explored for the potential to yield a disease
suppressive soil. Composts have been the
most commonly used substrate in this
context and extensive literature exists
concerning development and utilization of
plant-based composts for control of soil-
borne plant diseases (Hoitink and Boehm,
1999; van der Gaag et al., 2007). These
organic substrates have demonstrated signifi-
cant capacity to induce disease suppression
in defined environment or growth media
conditions (Mandelbaum and Hadar, 1990;
Widmer et al., 1998). However, while it may
be arguable, there has been minimal effective
use of such materials in field-level produc-
tion agriculture for this intended purpose.
There is no doubt that composts are utilized
in a multitude of plant production systems,
but consistently and predictably realizing the
intended goal, that being the development of
soil suppressiveness, has been elusive due to
an inability to predict effects on soil biological
composition and function. This in part can
be attributed to variability in consistency of
compost activity, which is a function of
multiple factors including substrate compos-
ition (Termorshuizen et al., 2006), storage
conditions (van Rijn et al., 2007) and curing
duration (Danon et al., 2007). Disease control
achieved with any given compost may also be
a consequence of host-mediated effects (van
Rijn, 2007). In addition, there exists the
potential that organic amendments including­
206 M. Mazzola
composts will yield not only increases in the
microbial consortia responsible for potential
disease suppression, but may also enhance
disease development due to an increase in
populations or activity of non-target or
target plant pathogens (Cohen et al., 2005;
Termorshuizen et al., 2006; Mazzola et al.,
2009).
That being said, there are significant
opportunities to utilize more clearly defined
bio-based products to enhance specific
processes including soilborne disease
suppression. By ‘clearly defined’, reference is
being made to the consistency of product
composition which will enable reproducibil-
ity of function, and a capacity to determine
functional mechanism(s) involved in such
processes. Certain of these amendments,
such as fish emulsion or bone meal, operate
primarily, though perhaps not exclusively,
through chemical mechanisms (Tenuta and
Lazarovits, 2004; Abbasi, et al., 2009).
However, there are other examples in which
the use of residues from specific sources,
such as an individual plant species, act to
selectively modulate the resident biology in a
manner that yields a suppressive soil.
Residues from plants belonging to the family
Brassicaceae have been studied extensively
for their potential to yield suppression of
various plant pests including pathogens,
insects and weeds (Brown and Morra, 1997).
Active interest in these plant residues as a
soil amendment emanated from the fact that
members of this plant family produce
glucosinolates which, upon hydrolysis, yield
several biologically active compounds, includ-
ing isothiocyanates. Chemical mechanisms
have long been viewed as the dominant mode
leading to pest suppression as a result of
brassicaceous amendments (Matthiessen
and Kirkegaard, 2006). However, several
studies have revealed that other functional
mechanisms operate to yield pest control. In
some instances soilborne disease and weed
suppression obtained in response to specific
brassicaceous amendments is not chemically
mediated but rather functions at least in part
through the resident soil biology (Mazzola et
al., 2001; Hoagland et al., 2008).
Brassicaceous seed meal amendments
effectively control a number of soilborne
diseases (Smolinska et al., 1997; Mazzola et
al., 2001; Chung et al., 2002). The operative
mechanism(s) differs according to the target
pathogen and seed meal plant source
(Mazzola et al., 2007a), and in certain
instances disease control requires specific
changes in microbial community compos-
ition that yield soil suppressiveness (Cohen
and Mazzola, 2006; Mazzola et al., 2007a).
Another level of complexity is realized when
the temporal nature of disease suppression is
examined and changes in functional
mechanism(s) are revealed. This phenom-
enon has been most apparent in seed meal-
induced control of Rhizoctonia root rot of
apple where several lines of support impli-
cated the need for a functional microbial
community to attain seed meal-induced
disease suppression. Such evidence includes
the fact that Brassica napus seed meal (BnSM)
provided disease control irrespective of
glucosinolate content; the capacity of BnSM
amendment to suppress Rhizoctonia root rot
was abolished if soil was pasteurized prior to
introduction of the pathogen, and only seed
meals such as BnSM, but not soybean meal,
which significantly elevated densities of resi-
dent Streptomyces spp. provided effective
disease suppression (Mazzola et al., 2001;
Cohen et al., 2005). Introduction of individ-
ual Streptomyces sp. isolates from seed meal
amended soils provided a level of disease
control that was equivalent to BnSM amend-
ment, and the majority of Streptomyces
isolates provided control of Rhizoctonia solani
through the induction of host defence
responses (Cohen and Mazzola, 2006).
In Brassica juncea seed meal (BjSM)
amended soil, the temporal dynamics in
elevation of resident Streptomyces popula-
tions corresponded with the induction of
soil suppressiveness, providing further
support for this phenomenon as a functional
mechanism. Disease control in response to
BjSM amendment was attained even in
pasteurized soil, but only if the amendment
was made at the time of pathogen infest-
ation. When addition of R. solani inoculum
was delayed until 24 h post-seed meal
amendment, pathogen suppression in native
(Fig. 11.1) or pasteurized soil was not
observed. The pattern of observed disease
 Soil Microbial Community Management 207

suppression corresponded with the pattern Streptomyces spp. populations (Mazzola et

of allyl isothiocyanate (AITC) generation, a al., 2007a). Seed meal-induced soil suppres-
process that was completed within 24 h of siveness towards Rhizoctonia root rot of
seed meal amendment (Mazzola et al., apple was also obtained in field trials through
2007a). Soil suppressiveness to Rhizoctonia the use of various brassicaceous seed meals
root rot was restored to native soils when including that of B. napus (Mazzola and
incubated for a period of 4 weeks, and the Mullinix, 2005; Fig. 11.2).
re-establishment of disease suppression was Accumulating data demonstrate that soil
associated with the elevation of resident biology may also contribute to seed meal-

BjSM 4 wk

BjSM 24 h

BjSM 0 h

Control

100 80 60 40 20 0 0 1 2 3 4 5 6 7 8
Rhizoctonia solani root infection (%) Streptomyces population (log cfu/g soil)

Fig. 11.1.  Duration of Brassica juncea seed meal (Bj SM) incubation period in soil prior to pathogen
infestation affects native Streptomyces densities, level of Rhizoctonia solani AG-5 infection of apple seedling
roots and mode of disease suppression induced by the seed meal amendment. Relative to a non-treated
control, disease was suppressed when the pathogen was introduced into soil at the time of seed meal
amendment (Bj SM 0h) or at 4 weeks after amendment (Bj SM 4 wk) but not when the pathogen was
introduced at 24 h after application of the amendment (Bj SM 24 h) (left panel). Populations (colony forming
units, cfu) of resident Streptomyces spp. in the corresponding soils, and their proliferation at 4 weeks post-
seed meal amendment are evident (right panel). Disease suppression attained when the pathogen was
introduced at the time of seed meal amendment (0 h) was attributed to the generation of allyl
isothiocyanate, but this chemical was evacuated from the system by 24 h post-seed meal amendment
(Mazzola et al., 2007a). Disease suppression attained when the pathogen was introduced at 4 weeks post-
seed meal amendment was attributed to the elevated populations and activity of resident Streptomyces.
Rhizoctonia solani root infection (%)

18
16 a
14
12 a
10
8
6
b b
4 b b
2
0
Control 1,3-D:C17 BnSM
Fig. 11.2.  Effect of soil treatment on Rhizoctonia solani infection of Gala/M26 and Golden Delicious/M7
roots in two apple orchards in Washington state: CV (black bars) and WVC (grey bars), respectively
(Mazzola and Mullinix, 2005). Soil fumigation and seed meal amendment significantly reduced root
infection relative to the non-treated control at both orchard sites (treatments with different letters differ
significantly P < 0.05), and there was no significant difference between seed meal and fumigation
treatments. BnSM, Brassica napus seed meal soil amendment; 1,3-D:C17, 1,3-dichloropropene-
chloropicrin soil fumigation.
208 M. Mazzola
induced suppression of root disease incited
by Pythium spp. BjSM effectively controls
Pythium root rot through the release of AITC
(Mazzola et al., 2009). However, other mech-
anisms of disease suppression must function
in a time-dependent manner as at least partial
disease control was attained in response to
seed meal amendment even when inoculum
of Pythium irregulare was introduced into soils
16 weeks post-seed meal amendment (Fig.
11.3.). Analysis of fungal communities using
a taxonomic macroarray indicated that
Trichoderma spp. were preferentially domin-
ant in amended soils suppressive to Pythium
whereas the fungal community was more
evenly distributed in soils conducive to
Pythium spp. (Izzo and Mazzola, 2007). It is
plausible that these fungi, which possess a
well-known capacity to provide biological
control of Pythium spp. (Howell, 1982;
Wolffhechel and Jensen, 1992), contributed
to the observed disease suppression.
Green manure systems to induce
biological soil suppressiveness
Green manures have been examined exten-
sively as a means to improve soil quality, but
although long studied (Millard and Taylor,
1927; Rouatt and Atkinson, 1950) this prac-
tice has been less effective or consistent
Pythium irregulare root infection (%)
90
80
70
60
50
40
30
20
10
0
Control
Fig. 11.3.  Effect of Brassica juncea seed meal (BjSM) on apple root infection incited by Pythium
irregulare when oospore inoculum of the pathogen (~2000 propagules/g soil) was introduced into the soil
system 16 weeks post-seed meal amendment. Coarse (2–4 mm diameter) and fine (< 1 mm diameter)
seed meal particles were used in the assay.
when applied to a system for the control of
soilborne diseases. As with certain organic
residue amendments, green manuring may
exacerbate disease development if used in
concert with an inappropriate pathosystem
(Manici et al., 2004). The lack of consistency
can be attributed to various factors, most
being similar to those limiting the efficacy of
organic residue soil amendments detailed
above, including an absence of knowledge
concerning the underlying mechanisms of
the organic-matter-mediated disease sup­pres­
sion. As a result, incorporation of green
manure crops into soil with the intended goal
of specifically managing disease suppressive
elements of the resident soil microbial
community has received minimal study.
The incorporation of green manures has
been shown to increase the diversity and
density of certain microbes known to have
pathogen inhibitory activity, including fluor-
escent Pseudomonas spp., non-pathogenic
Fusarium spp. and Streptomyces spp. However,
within resident populations of each of these
microbial communities numerous members
will inherently lack one or more of the func-
tional attributes that confer capacity to limit
disease incited by any given pathogen
(Larkin and Fravel, 1999; Gu and Mazzola,
2003; Zhao et al., 2009). Thus, as in the use
of bio-based soil amendments, identification
of operative mechanisms and the ability to
BjSM fine BjSM coarse
Soil treatment
 Soil Microbial Community Management 209
monitor the relative presence of the attribute
in native soil microbial populations will be
intrinsic to the successful application of
green manuring as a means to induce biolog-
ically based disease suppressive soils.
Kinkel and colleagues have been at the
forefront in attempts to discern the mech-
anisms of biologically mediated disease
suppressive soils developing in response to
green manuring. In particular, studies have
focused on the contribution of the resident
Streptomyces community towards the induc-
tion of soil suppressiveness in response to
green manures. A green manure crop of
buckwheat or canola increased the propor-
tion of streptomycetes in the resident popu-
lation that were antagonistic towards the
potato pathogens Streptomyces scabies,
Verticillium dahliae and R. solani (Wiggins
and Kinkel, 2005a). The relative increase in
inhibitory activity of the streptomycete
community was frequently associated with a
decrease in disease development and an
increase in potato yields. Similar increases
in the proportion of antagonistic strepto-
mycetes and reduction in lucerne root rot
were observed in buckwheat or sorghum–
sudan grass-treated soils (Wiggins and
Kinkel, 2005b). Buckwheat and sorghum–
sudan grass green manures also increased
the density and inhibitory activity of resi-
dent bacterial populations and Streptomyces
spp. expressing antagonistic action towards
the causal pathogen of Fusarium head blight
of wheat, F. graminearum (Perez et al., 2008).
As an initial step in the process towards
developing a protocol for selection of appro-
priate green manure crops (or other resource
amendments) for the generation of a highly
inhibitory soil microbial community, studies
were conducted to explore the effects of
specific types and quantities of C compounds
on resident populations of Streptomyces spp.,
and their antagonistic potential (Schlatter et
al., 2009). Addition of complex C sources
tended to yield greater Streptomyces densi-
ties than the simple sugar glucose. Higher
inputs in the form of these C sources resulted
in a Streptomyces community with greater
antibiotic inhibitory activity than when soil
was treated at a lower input level. In this
system, further characterization of the
means by which specific nutrient inputs
influence Streptomyces inhibitory activity
may enhance the ability to actively manage
disease suppressive soils through the green
manure management programmes.
Cropping systems to mediate biologically
based soil suppressiveness
Several modifications to crop production
systems have been employed as a means to
control soilborne plant diseases. The most
common and effective scheme has been the
use of crop rotations, with disease control
believed to be achieved as the absence of a
suitable plant host results in diminished
viability of the pathogen. Attempts to develop
specific cropping models to manage the resi-
dent soil microbiota for disease suppression
have been few. It has been reasoned that as
increased plant diversity can enhance micro-
bial community biomass (Zak et al., 2003)
mixed cropping systems will generate a more
diverse microbial community and thus should
be more resilient to pathogen invasion
(Workneh and van Bruggen, 1994; Hiddink et
al., 2005). However, the preponderance of
examples of induced suppressive soils come
from crop monoculture systems (Chet and
Baker, 1980; Cook and Weller, 1987), and
limited attempts to compare mixed crop
systems with single crop systems indicate
that mixed systems may not enhance micro-
bial diversity or disease suppressiveness
(Hiddink et al., 2005).
Plant root systems and their release of a
complement of root exudates serve as a
dominant driving force in determining soil
microbial community diversity and density
(Lemanceau et al., 1995; Dalmastri et al.,
1999; Miethling et al., 2000; Marschner et
al., 2001; Berg et al., 2002; Mazzola and Gu,
2002), particularly in conventional crop
production systems where organic matter
and substrate availability is typically
nominal. As noted above, certain crop mono-
culture systems express the ability to select
for microbial communities that over time
lead to the development of soils suppressive
to specific soilborne pathogens (Larkin et al.,
1993; Weller et al., 2002). Alternatively,
210 M. Mazzola
previous cropping systems may inadvert-
ently yield a soil suppressive to a pathosys-
tem of a subsequent unrelated crop. For
example a soil cropped to a continuous
wheat monoculture was shown to be
bio­logically suppressive to Rhizoctonia root
rot of apple incited by R. solani AG-5
(Mazzola, 1999). Once planted to apple, soil
suppressiveness towards this pathogen
diminished over time and loss of disease
suppression corresponded with specific
changes in composition of the fluorescent
Pseudomonas spp. population and reduced
densities of Burkholderia cepacia recovered
from orchard soils. Interestingly, soil
suppressiveness towards Rhizoctonia root
rot of both apple and wheat could be restored
in greenhouse trials through repeated culti-
vation of these soils with wheat (Mazzola
and Gu, 2000, 2002). Restoration of soil
suppressiveness was associated with a trans-
formation of the fluorescent pseudomonad
community to one that more closely resem-
bled that initially recovered from the field
suppressive soil.
Although extended cultivation of apple
selected for a microbial community lacking
apparent inhibitory activity towards soil-
borne fungal pathogens (Mazzola, 1999),
this does not appear to be a universal
response in perennial plant production
systems. Long-term grapevine monoculture
enriched the soil with fluorescent
pseudomonad­ genotypes that produce
2,4-DAPG and hydrogen cyanide (HCN)
(Svercel et al., 2009), bacterial characteris-
tics which have been repeatedly associated
with disease suppressive soils (Haas and
Défago, 2005). While the duration of grape-
vine monoculture examined in this study
was excessive, with certain sites planted
since the first millennium without interrup-
tion, this example does demonstrate again
the capacity of crop monoculture to selec-
tively enhance microbial communities func-
tional in the development of disease
suppressive soils.
In an evaluation of organic cropping
systems, Postma et al. (2008) reported
significant differences in soil suppressive-
ness towards multiple pathogens, including
R. solani AG 2.2IIIB, which is an important
pathogen of sugarbeet. Disease suppression
was elevated in systems that employed a
grass–clover sequence within the rotation
cycle, and suppressiveness lasted 2 years
beyond this sequence but disappeared after
3 years. The development of soil suppres-
siveness in this system was correlated with a
significant increase in Lysobacter spp. popu-
lations. Lysobacter spp. produce a number of
lytic enzymes and antibiotics that account
for their capacity to provide biological
control of various fungi and oomycetes
(Kobayashi et al., 2005). The association of
Rhizoctonia suppressiveness and Lysobacter
was re­stricted to clay soils and was not
detected in sandy soils (Postma et al., 2008).
Multiple aspects of a production system
have the capacity to limit or enhance the
adoption of plant-mediated induction of soil
suppressiveness as a viable practice for the
management of soilborne plant diseases.
Foremost among these is the time frame,
perceived or actual, required to bring about
the disease suppressive state. Different plant
species or genotypes have inherently differ-
ential abilities to select for microbial commu-
nities with the capacity to yield disease
suppression (Smith et al., 1999; Mazzola and
Gu, 2002; Mazzola et al., 2004; Berg et al.,
2005). Thus, plant species or genotype evalu-
ation will be instrumental to optimizing
densities of the functional microbial popula-
tion and reducing the time necessary to yield
a disease suppressive soil. 2,4-DAPG-
producing fluorescent pseudomonads have a
demonstrable role in the development of
soils suppressive to take-all of wheat (Weller
et al., 2002) and also have been isolated from
soils that naturally suppress black root rot of
tobacco (Keel et al., 1996; Ramette et al.,
2003) or Fusarium wilt disease (Landa et al.,
2002). Development of a take-all suppres-
sive soil requires a threshold population of
these bacteria (Raaijmakers et al., 1997) and
certain bacterial genotypes possess a
superior­ capacity to limit disease develop-
ment (Raaijmakers and Weller, 2001).
Plant genotypes were shown to differ in
both the ability to enrich for populations of
indigenous 2,4-DAPG-producing fluorescent
pseudomonads and the dominant bacterial
genotype that was supported in the
 Soil Microbial Community Management 211

rhizosphere­ (Mazzola et al., 2004; Picard et (Mazzola and Gu, 2002). The two effective
al., 2008). In addition, expression of wheat cultivars, ‘Lewjain’ and ‘Penawawa’,
2,4-DAPG biosynthetic genes in the rhizo- altered the genetic and species composition
sphere is influenced by plant genotype (Notz of the fluorescent pseudomonad community
et al., 2001; Jamali et al., 2009). Thus, effort resident in the wheat-cropped orchard soils
to select for plant genotypes that possess a (Mazzola and Gu, 2002; Gu and Mazzola,
greater capacity to stimulate resident popu- 2003). The fluorescent Pseudomonas spp.
lations of effective 2,4-DAPG-producing population from the resulting suppressive
fluorescent pseudomonad genotypes, or soils demonstrated a significantly greater
other functional genotypes, should be of degree of antagonism towards R. solani than
benefit in systems that seek to utilize crop- did the population from non-treated control
ping systems as a means to induce disease soil or soils cultivated with wheat genotypes
suppressive soils. that were ineffective in the induction of soil
The importance of plant genotype in deter- sup­pressive­ness.
mining the development of a biologically In subsequent studies, the capacity of
suppressive soil has been demonstrated in continuous wheat cropping as a means to
multiple systems. The capacity of continuous effectively control Rhizoctonia root rot of
cropping of watermelon to induce soil apple was demonstrated in field trials
suppressiveness to Fusarium wilt was cultivar (Mazzola and Mullinix, 2005). In this
dependent (Larkin et al., 1993). Furthermore, system, a three-cultivar seed mixture was
plant genotype was shown to be a significant used in the cropping of wheat on a replant
factor in the capacity of wheat cultivation to apple orchard site with three successive
yield a soil microbial community suppressive 10-week growth cycles. At the end of each
towards Rhizoctonia root rot of wheat and growth cycle plant biomass was removed
apple (Mazzola and Gu, 2002). Among five prior to replanting the site, and at the end of
genotypes evaluated, only two were shown to the third wheat cycle the orchard was planted
consistently generate a soil biologically to Gala/M26 apple. Under this practice,
suppressive towards Rhizoctonia root rot in Rhizoctonia root infection was significantly
response to successive wheat growth cycles reduced (Fig. 11.4) and the wheat cropping

25
Rhizoctonia solani root infection (%)

a
20 a
a
15 ab

10
bc
c
5 c
c
0
Control MeBr Fallow Wheat Cgm Cgm Cgm Cgm
(3 years) (1 year) (1 year) (2 years) (3 years) (2 years)
– wheat
(1 year)
Soil treatment
Fig. 11.4.  Effect of soil treatments on incidence of Rhizoctonia solani infection of Gala/M26 apple roots
at CV orchard, Orondo, Washington state (Mazzola and Mullinix, 2005). Bars designated with the same
letter do not differ significantly (P > 0.05). MeBr, pre-plant methyl bromide soil fumigation; Wheat (1 year),
mixed cultivar cover crop grown for three successive 10-week plantings followed by removal of plant
biomass; Cgm, canola green manure with soil incorporation of plant biomass.
212 M. Mazzola
procedure was more effective than a 1- or
2-year canola green manure in suppressing
this root disease. The 3-year canola green
manure was as effective as the wheat-
cropping­scheme in limiting apple root infec-
tion by Rhizoctonia spp.
Conclusions
Active management of the biological
resources native to agricultural soil ecosys-
tems is a logical progression in our studies of
the basis for the function of disease suppres-
sive soils. While studies of disease suppres-
sive soils have provided a wealth of
information concerning the source of
biological activity there has been relatively
little progress in our capacity to manage the
effective microbial resources indigenous to
agricultural ecosystems. Rather, focus has
remained on isolation and identification of
the numerous biologically active microbial
agents resident in such soils, and subse-
quently resorting to the inundative release of
these microorganisms into non-native soils
or crop production systems. Climate change
undoubtedly will have an effect on many
biological processes leading to altered ecosys-
tem function. Such changes are predicted to
modulate the efficacy of certain strategies
that are commonly utilized for the manage-
ment of soilborne diseases. In concert with
the loss or impending restricted use of
numerous chemicals (e.g. methyl bromide)
previously used for soilborne disease control,
it seems an appropriate time to further
examine the prospect for managing ecosys-
tem microbial resources as a viable soilborne
disease control strategy. While climate
change is bound to have impacts on the soil
biology that is functional in disease suppres-
sive soils, pathogen populations will acclima-
tize to these changes concurrently with the
resident microbial milieu and thus effective
adaptive traits are likely to reside across
these broad communities.
In the development of protocols for the
management of disease suppressive soil
biology, it may be useful to consider the
similar efforts pursued within the field of
bioremediation and the comparable
impediments­ to effective use of specific
plant-mediated strategies. Specific plant
systems are designed not only for phyto­
extraction of pollutants but also as a means
to secure the value of microbial partners
that possess the ability to degrade organic
pollutants. Much as is the case in phytore-
mediation efforts, little emphasis has been
placed on breeding efforts towards the devel-
opment of crop genotypes with an elevated
capacity to select for specific microbial geno-
types functional in disease suppression.
Reluctance to pursue plant breeding
programmes focused on such attributes was
limited until recently by a lack of acceptance
or understanding of this phenomenon as a
valuable parameter to crop improvement.
Molecular plant breeding programmes
are at the head in the development of plants
with enhanced capacity to select for plant
beneficial microbial communities, including
those involved in disease suppression.
Multiple recent examples demonstrate the
potential of this approach. A transgenic
tobacco overexpressing ferritin imposed
reduced iron availability in the rhizosphere
resulting in a fluorescent pseudomonad
community with a greater ability to grow
under iron stress conditions. This resulting
bacterial population possessed a greater
capacity to inhibit growth of the plant path-
ogen Pythium aphanidermatum (Robin et al.,
2007). Genetic modification of the wheat
cultivar ‘Bobwhite’ by insertion of the
powdery mildew resistance gene Pm3b
resulted in multiple transgenic lines with an
enhanced capacity, relative to the parental
line, to select for 2,4-DAPG-producing fluor-
escent pseudomonads (Meyer et al., 2009).
Thus, evidence indicates that efforts to
develop crop cultivars with an elevated
potential to exploit the resident disease
suppressive microbial community are not
futile, and in fact will be worthwhile for the
development of more sustainable crop
production systems.
Strategies other than those discussed
here have received a modicum of research
investigation but may effectively serve to
manage microbial resources resident in agro-
ecosystems in a manner to suppress soil-
borne plant diseases. In addition to the use
 Soil Microbial Community Management 213
of organic amendments or the design of
specific cropping sequences, further meth-
ods such as fertility management, crop resi-
due management and soil tillage (Peters et
al., 2003) may function to enhance soil
suppressiveness. While adaptation of these
cultural practices to increase the level of soil
suppressiveness is receiving increased atten-
tion as a potential soilborne disease control
practice, there has been only minimal consid-
eration of the effect of such treatments on
overall soil biology composition and func-
tion.
It is a daunting task to envision develop-
ment of management systems to yield
biologically suppressive soils for diseases in
which such soils have not previously been
characterized. Such an undertaking requires
initial focus on identification of the micro-
bial attributes that function to elicit disease
suppression. Although such investigations
continue to be a complex and protracted
process, emerging tools in molecular micro-
bial ecology, including metagenomics and
pyrosequencing will enable more rapid evalu-
ation of microbial community structure, and
ultimately function (van Elsas et al., 2008).
Such analytical tools will enable more
complete examination of resident soil biol-
ogy, changes to such populations in response
to specific practices, and comparative micro-
bial community analysis among soils allow-
ing one to more reliably predict microbial
effectors of disease suppression. These same
methods will enable more efficient analysis
of microbial community structure in response
to agroecosystem management practices and
enable prediction of the resulting benefits to
plant growth through disease suppression. A
greater understanding of the consequence of
such treatments on food webs that modulate
the density and activity of microbial popula-
tions functional in disease control will be
instrumental to the development and even-
tual adoption of tools for the management of
disease suppressive soil biology.
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12
Biotechnology in Agriculture

Ryan Whitford, Michael Gilbert and

Peter Langridge

Abstract
Climate change is predicted to result in disruption of many farming systems. The Food and Agriculture
Organization (FAO) predicts a 15–20% fall in global agricultural production by 2080. Consequently,
adaptation of major crop species to climate change will be the biggest challenge for plant breeders this
century. Biotechnology will be important when adapting crops to better tolerate changing stresses. It
includes using advanced genetic mapping technologies, like molecular markers, in the breeding and
development of new varieties. Molecular markers are used to provide greater focus, accuracy and
speed in crop breeding programmes with further advances coming. Genetic modification (GM)
techniques are providing access to a diversity of genes, used to develop plant varieties more tolerant
to the negative impacts of climate change.

What is Biotechnology?

Biotechnology is the targeted modification

of living organisms and is used widely in ge
Rate of change

agriculture. It includes tools used to under- han

c
e
stand and manipulate the genetic make-up at
of organisms used for producing or process- lim Technology gap
c ns
of lutio
ing agricultural products. ct
s so
Increasingly, extreme climatic events will ffe e ding
E bre
impact on food production in many areas of ional
ent
the world. A +1°C local temperature change C onv
may threaten rainfed cereal production while
Time
changes of over +3°C will lead to major crop
losses (Easterling et al., 2007). Adaptation in Fig. 12.1.  Keeping pace with climate change.
management may partially mitigate against
these effects but biotechnology may also be Nature of adaptive change
used to improve resistance to pests and
diseases, improve yield stability, reduce reli- Biological organisms undergo adaptive
ance on fertilizer and enhance the nutri- change as they acclimatize to new environ-
tional value of staple crops. ments. Many adaptive characteristics result
A rapidly changing climate will require from the prevailing environment influenc-
rapid development of new plant varieties; ing expression of genes related to adapta-
biotechnology can enhance the speed, flexi- tion. Genes are also subject to constant
bility and efficiency of plant breeding (Fig. change; random changes or ‘mutations’ can
12.1). occur through internal errors in DNA repair

© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 219
220 R. Whitford et al.
and replication or when subjected to external
influences such as ultraviolet irradiation.
These mutations can alter expression or
activity of encoded proteins.
Within any population of plants there is
genetic variation: natural or induced. Over
many centuries, farmers have generated
heterogeneous plant populations adapted to
local climates and cultivation conditions.
More recently, plant breeders have selected
superior variants to generate genetically
homogenous, highly adapted, ‘elite’ cultivars.
Intense cereal breeding has resulted in
spectacular improvements in yield and qual-
ity but has narrowed genetic diversity.
Continued genetic gain is becoming increas-
ingly difficult (Feuillet et al., 2008). Using
biotechnology, plant breeders have sought
to identify and deploy new sources of vari­
ation by understanding the available genetic
variation, the genetic control of adaptation,
and the gene-by-environment interactions.
Plant responses to different environ-
ments are not thoroughly understood nor
are their genetic bases. Studies of funda-
mental adaptation mechanisms have focused
on single, rather than multiple, genotype–
stress relationships. Many have also exam-
ined plant survival under extreme stress
rather than more realistic, agronomically
relevant, stress scenarios (Cushman and
Bohnert, 2000; Bartels and Salamini, 2001;
Araus et al., 2003).
Adapting to drought stress is a huge chal-
lenge in plant breeding because ‘drought’
means many different things. Stresses may
be caused during grain filling, pre-flowering
or may be continuous throughout a growing
season. In Mediterranean-type dryland
areas, grain-filling stress is common, in South
America pre-flowering stress is more likely
and continuous stress is frequent in non-
irrigated parts of southern Asia where plants
are often dependent upon water stored in
the soil (Reynolds et al., 2005). Plants often
face multiple stresses concurrently; under
water-limiting conditions, there may also be
high temperatures, increased irradiance and
less permeable soil. These factors make the
plant breeder’s task very complex, and
breeders­ must grapple with drought-related
stresses most relevant to them.
Variation
Natural genetic variation
Introgression
Genetic variation can be exploited by intro-
gression; genes are moved into the cultivated
gene pool by continuously backcrossing with
the cultivated parent. While this takes many
generations, it is the most widely adopted
method for expanding available variation in
a breeding programme. However, it can be a
slow process.
Example 1: Improved resistance of cultivated
European spring barley to mildew has been
achieved by introgressing an Ethiopian landrace
mlo-11 (Jørgensen, 1992). Norman Borlaug
successfully introgressed Rht semi-dwarfing
genes from the Japanese variety Norin-10 into
elite wheat varieties resulting in the 1960s
‘Green Revolution’ (Ellis et al., 2007).
‘Linkage drag’ is the simultaneous introgres-
sion of deleterious alleles. Introgression of
chromosome regions from landraces or wild
relatives can be a slow and complex process
because just the minimal region needs to be
introduced. Biotechnology, particularly
through the use of molecular markers, plays
a key role in accelerating this process.
Example 2: Rye chromosome fragment 1RS
contains genes responsible for improved grain
yield, race-specific rust resistance, improved
adaptation and stress tolerance (Zarco-
Hernandez et al., 2005). When introgressed into
wheat, the 1RS/1BL translocation in wheat
negatively impacts gluten strength: it makes
bread dough ‘sticky’.
Amphiploids
Entire chromosomes or even entire genomes
can be added as an alternative to introgres-
sion. Genetic diversity in intensively bred
species, such as wheat, can be exploited.
 Biotechnology in Agriculture 221
Example 3: In 1938, the first fertile ‘Triticale’
(Triticosecale) exhibited improved yield and
adaptability to regions not suitable for wheat
production (Feuillet et al., 2008). This repro-
duced a naturally occurring process exploited
by early farmers to develop many modern crop
species such as hexaploid wheat, tetraploid
potatoes and tetraploid cotton. Genome analy-
sis has shown that even maize and rice are
ancient tetraploids. ‘Synthetic hexaploid wheats’
can be generated by hybridizing durum wheat
(AABB) with Aegilops tauschii (DD). Breeding
programmes have produced more than 1000
‘synthetic wheats’ and are an important source
of genetic diversity (CIMMYT, 2009b).
Induced genetic variation
Sexual reproduction has many barriers, such
as hybrid infertility, that prevent the use of
wild germplasm in plant breeding.
Mutagenesis can be used to induce, or create,
new genetic variability.
Mutagenesis
Radiation, such as gamma-rays, or chemicals
such as alkylalkanesulfonates, can be used
to generate variation from which plants with
desirable characteristics can be selected.
Example 4: The first successful mutant barley
with ‘stiff straw’ (cultivar ‘Pallas’, 1958) was
generated because of a new process: combine
harvesting (Lundqvist, 1986). A gamma-irradi-
ated malting-cultivar mutant was selected for its
semi-dwarf growth habit and cultivar ‘Golden
Promise’ became the dominant malting quality
barley in Scotland throughout the 1970s and
1980s (Forster et al., 1997).
In vitro culture
In vitro culture of totipotent plant cells and
tissues has increased the importance of the
laboratory in plant breeding. In vitro culture
of haploid microspores, or ‘androgenesis’, is
used to produce doubled haploids for genetic
mapping; this is important when decipher-
ing the relationship between genetic vari-
ation and agronomic traits. Doubled haploidy
enables complete homozygosis in one gener-
ation rather than recurrent backcrossing for
six or more generations, as is usually
required; many breeding programmes use
this technique to accelerate the delivery of
homozygous lines for release.
In vitro culture can be used to induce soma-
clonal variation such as changes in chromo-
some number (polyploidy, aneuploidy),
chromosome structure (translocations, dele-
tions, insertions and duplications) and DNA
sequence (base mutations). This has been
useful for introgressing ‘alien’ genes.
Example 5: A cereal cyst nematode resistance
was transferred from rye into wheat by the in
vitro culture of wheat–rye monosomic addition
lines (Larkin et al., 1989; Banks et al., 1995).
Insertional mutagenesis
Insertional mutagenesis uses foreign DNA
fragments to disrupt gene function.
Agrobacterium-mediated gene transfer has
been widely applied for generating such
mutations and has been used to support
gene discovery programmes.
Role of Biotechnology
Advances in molecular biology have resulted
in rapid identification and quantification of
genetic variation as well as identification of
genes or genomic regions associated with
the expression of qualitative and quantita-
tive traits (Fig. 12.2).
Building knowledge and understanding
An ‘explosion’ in plant genetics and genom-
ics research as well as the quantity of infor-
mation about plant genome structure, has
resulted in a ‘technology gap’. Resource
development has exceeded the ability to
solve practical plant breeding problems
using those resources. This gap is being
closed by providing tools and methods to
breeders to help them identify, and select,
traits and underlying genes.
222 R. Whitford et al.
Improving
diversity and
population
dynamics
Better
Developing
new crop understanding
of adaptive
breeding
strategies change
mechanisms
Generating
genetically
modified
plants
Fig. 12.2.  How biotechnology helps breeding.
Understanding mechanisms and processes
Biotechnology helps us understand the
effects of simultaneous multiple, complex
stresses, such as drought, where multiple
signalling pathways are activated and specific
responses cannot always be assigned to an
individual stress. Transcript profiling can be
used to classify stress responses: for exam-
ple osmotic stress responses can be initiated
via either an abscisic acid (ABA)-dependent
or an independent signalling pathway (Gosti
et al., 1995; Ishitani et al., 1997).
Example 6: A reduction in leaf water causes a
passive loss in guard cell turgor, reducing photo-
synthetic activity, and, with increased irradiance,
an excess of reactive oxygen species (ROS).
These are toxic to cellular metabolism. Plants
produce chemical antioxidants such as ascorbic
acid, glutathione and α-tocopherol as well as
enzymes such as peroxidases and superoxide
dismutases capable of detoxifying ROS. Turgor
is managed by subcellular sequestration of ions
such as Na+ and K+ into the vacuole and by
synthesizing osmolytes (reviewed by Langridge
et al., 2006).
It is unclear which physiological or molecu-
lar processes need to be modified, or selected
for, to improve crop productivity under
drought stress. There is controversy about
the value of selection for osmotic adjust-
ment and ABA response; a systematic trait
orientated breeding approach is required in
order to fully exploit these genetic mech-
anisms (Reynolds et al., 2005).
Example 7: Identification of the disaccharide,
trehalose, from desert resurrection species has
helped to classify non-reducing disaccharides
as osmoprotectants functionally important for
drought tolerance. Understanding the physiol-
ogy of trehalose accumulation has led to an
improvement in drought tolerance of species
such as rice, potato and tomato. These findings
show that novel physiological traits can be used
for selection (Almeida et al., 2007).
Biotechnologies are tools used to identify,
classify and select these traits.
Plant modelling
Plant breeding predicts phenotypes, based
on genotypes, by measuring phenotypic
performance in large segregating popula-
tions and then applying statistical pro­cedures
based on quantitative genetic theory.
Plant modelling can link phenotypic and
physiological/molecular knowledge.
Example 8: Modelling of osmotic adjustment in
sorghum identified the functional mode of
action, and estimated yield advantages of up to
5% across multiple stress environments
(Hammer et al., 1999). Plant modelling can be
also used to develop alternative breeding strat-
egies (Chapman et al., 2003). Kuchel et al.
(2005) used computer simulation to design a
genetically effective, economically efficient
marker-assisted wheat breeding strategy.
Significant genetic gains in yield, end-use qual-
ity and disease resistance resulted.
Gene network models, while less common,
may predict the consequences of altering
specific gene sequences and protein modifi-
cations.
Example 9: Flowering-time transition models in
Arabidopsis (Koornneef et al., 1998; Welch et
al., 2003) laid the foundation for gene-sequence-
based predictive modelling, which is now
applied to predict sorghum flowering time. The
simulation model predicted grain yield, from two
allelic variants of sorghum, for a number of
specific environments (Hammer et al., 2008).
 Biotechnology in Agriculture 223

Yield potential and stability Supporting conventional breeding

Molecular processes underlying yield poten-
tial and stability have primarily targeted
increasing source and sink strengths and the
modifications of assimilate partitioning,
plant architecture and development (Van
Camp, 2005). Little progress has been made
in quantitatively identifying genetic compo-
nents that define yield.
Strategies to enhance yield per se may
include:
1. Introducing more efficient C4-like photo-
synthesis from maize into C3 rice. So far,
these approaches have not resulted in full C4
photosynthesis despite maize having a close
evolutionary relatedness to rice. Combining
the expression of two C4 enzymes (phos-
phoenolpyruvate carboxylase and pyruvate
orthophosphate dikinase) has, however,
resulted in increases of 35% in photosyn-
thetic capacity and 22% in yield (Ku et al.,
2001).
2. Introducing variants of Rubisco, a key
enzyme for carbon fixation, with a higher
catalytic rate and/or better discrimination
between gaseous substrates. Manipulating
Rubisco activase by targeting the synthesis
or degradation of inhibitors may modulate
Rubisco activity and control its stability
under stress. Some chimeric and mutant
versions of Rubisco activase are less heat
labile and, when reintroduced back into
Arabidopsis, have improved photosynthesis
and leaf growth under heat stress (Kurek et
al., 2007; Portis et al., 2007).
3. Increased endosperm ADP-glucose pyro-
phosphorylase activity. Yield enhancement
of more than 20% occurred when wheat and
rice were modified for this rate-limiting
enzyme in endosperm starch synthesis, an
important determinant of sink strength.
Screening
Breeding programmes often grow thou-
sands, or millions, of individual plants to
increase the probability of identifying indi-
vidual plants with specific gene combina-
tions; this requires new tools, some
biotechnological, for plant selection.
Isozyme markers were used in the 1980s
to hasten the introgression of monogenic
traits from wild germplasm into a cultivated
background, a process now known as marker
assisted selection (MAS) and now based
around the direct detection of variation in
DNA sequences (Table 12.1). This can be
used to indirectly select traits by detecting
genetic variation closely linked to underly-
ing genes.
marker-assisted backcrossing  The use of
molecular markers is justified when conven-
tional phenotypic trait selection is difficult,
or is dependent on specific environments or
developmental stages that influence the
expression of the target phenotype (Xu and
Crouch, 2008). MAS can hasten backcross-
ing and is useful in maintaining recessive
alleles.
Example 10: Marker-assisted backcrossing
(MABC) of Sub1, a major quantitative trait locus
(QTL) on chromosome 9 of rice, has improved
submergence tolerance of ‘Swarna’, a cultivar
widely grown in flood-prone regions of Asia
(Neeraja et al., 2007). Simple sequence repeat
(SSR) markers aided both the introgression of
Sub1 and the subsequent recovery of the recur-
rent parental background. Introgression of Sub1
converted ‘Swarna’ to a submergence-tolerant
variety within three backcross generations (2–3
years).

Table 12.1. Recent marker systems developed and applied to marker

assisted selection (MAS).
Acronym Description
RFLPs Restriction fragment length polymorphisms
RAPDs Random amplified length polymorphisms
STS Sequence tagged site
AFLPs Amplified fragment length polymorphisms
SSRs Simple sequence repeats or ‘microsatellites’
SNPs Single nucleotide polymorphisms
224 R. Whitford et al.
marker-assisted pyramiding  MAS may be
used to pyramid multiple monogenic traits,
or several QTLs for a single target trait, with
complex inheritance such as drought toler-
ance. Root architecture is a secondary trait
intrinsically linked to drought tolerance.
Example 11: The effect of QTLs for root archi-
tecture on yield has been reported under vary-
ing moisture regimes in rice and maize (reviewed
by Collins et al., 2008). After the identification of
four major root architecture QTLs in rice, MAS
aided the introgression of all alleles for increased
root length from ‘Azucena’ into ‘Kalinga III’, an
upland variety (Steele et al., 2006, 2007).
early-generation mas  MAS is often simpler
than phenotypic screening selection and can
be carried out at early stages of development
and on single plants, rather than plant fami-
lies or plots. Using MAS to select in ‘off-
season’ nurseries enables cost-effective
production of more generations per year.
DNA extraction is the largest cost in MAS
and is often the primary rate-limiting factor
for scaling up the whole process (Xu and
Crouch, 2008).
Recent development of non-destructive
single seed-based DNA extraction and geno-
typing systems is enhancing MAS efficiency
significantly and is being applied to the
International Maize and Wheat
Improvement Center’s (CIMMYT) maize
molecular breeding programmes (Gao et al.,
2008).
metabolite-assisted breeding   Genomic-
based technologies such as metabolic profil-
ing are now used in addition to MAS. The
rapid development of high-throughput tools
for metabolite profiling makes DNA
sequence-based profiling cost competitive
(Kopka et al., 2004). Metabolite profiling
will assist in the selection of components of
yield and stress tolerance (Fernie and
Schauer, 2009).
Example 12: Important metabolic traits include
carotenoid content of tomato, protein content of
maize and starch content of both potato and
rice (Fernie and Schauer, 2009). High-
throughput metabolomic screening of large
tomato breeding populations for carotenoid
metabolites has used matrix-assisted laser
desorption ionization time-of-flight mass spec-
trometry (MALDI-TOF-MS). Profiling of lines
from two tomato populations (Solanum pennellii
introgression lines and saturated mutants) iden-
tified germplasm likely to assist breeding of fruit
containing high levels of nutriceuticals (Fraser
et al., 2007).
Combined MAS
Genetic gain can be improved when pheno-
typic selection is combined with MAS. Even
where relationships between gene informa-
tion and phenotypic variation are well
defined, a lack of appropriate computational
tools has hampered incorporation into
breeding programmes (Xu and Crouch,
2008). However, new simulation and deci-
sion-support software are enabling the inte-
gration of genomics into breeding
programmes, increasing the scale, efficiency
and impact of MAS. Combining screening
technologies and computational modelling
should shorten the introduction of new
varieties by between 3 and 5 years.
Example 13: The genetics and breeding simu-
lation tool, QuLine/QuCIM, has been used by
wheat breeders to predict cross performance
and compare selection strategies (Wang et al.,
2003, 2007; Kuchel et al., 2005).
Analysis of diversity and population
dynamics
Applying molecular marker technologies to
large breeding programmes has advanced
genetic mapping; many QTLs controlling a
range of abiotic stresses have been identi-
fied.
 Biotechnology in Agriculture 225
SSRs, amplified fragment length poly-
morphisms (AFLPs) and random amplified
length polymorphisms (RAPDs) have been
used to assess genetic diversity in synthetic
wheat derivatives (Zhang et al., 2005) and
landraces (Strelchenko et al., 2004), import-
ant sources of abiotic stress tolerance.
Genotypic variation is used to improve
stress tolerance in elite germplasm. Superior
genotypes can be developed by the molecular
measurement of genetic similarity or genetic
distance between parents (Korzun, 2003).
Example 14: In common bean (Phaseolus
vulgaris L.), ultrametric genetic distances
between progeny and a target parent were used
in combination with nine indexed QTL-linked
markers, weighted according to the amount of
phenotypic variance they explained, to select
high-yielding lines that retained important QTLs
in a desirable genetic background (Tar’an et al.,
2003). Critical for this methodology was a
bio­informatic platform capable of compiling and
comparing complex molecular fingerprints and
delivering predictions of genetic distance and
variance.
Rapidly identifying genotypes using DNA-
based molecular marker technologies is help-
ing breeders to select elite genotypes without
extensive field-based testing (Reynolds et al.,
2009).
Abiotic stress tolerance diversity in wild
relatives and breeding populations is also
used to validate candidate genes.
Example 15: Collaboration between CIMMYT,
Cornell University and the Chinese, Kenyan,
Thai and Zimbabwean governments is identify-
ing key regulators in drought response pheno-
types from 350 tropical maize lines. Metabolites
such as sucrose, glucose, starch, ABA and the
ABA glucose ester of leaves and reproductive
organs are being assessed under both water-
stressed and well-watered conditions, alongside
yield components and secondary traits. The
genotypic component of the association test
involves haplotyping about 130 ABA and carbo-
hydrate synthesis pathway candidate genes
and drought-tolerance response genes involved
from maize and other plant species (Ribaut et
al., 2009). One- and two-dimensional gas chro-
matography/mass spectrometry (GC-MS) has
been used to survey 70 rice cultivars for import-
ant nutritional metabolites (Kusano et al., 2007;
Oryzabase, 2009).
Management of germplasm resources is a
major problem for many crop improvement
programmes. Diversity surveys help with
the compilation of smaller genotype-based
reference sets reflecting the allelic diversity
present in the larger germplasm reserves.
Example 16: The analysis of 3000 chickpea
accessions with 48 SSR markers revealed
extensive allelic diversity: 78% of all alleles were
captured in a reference set of 300 accessions
(Upadhyaya et al., 2008).
High-throughput technologies
(genotyping, phenotyping)
It typically takes 12 years to release a
commercial cereal variety from the time of
the initial cross, and perennials may take
longer. The increasing rate of climate change
requires accelerated breeding, now being
assisted by high-throughput genotyping and
phenotyping technologies.
Phenotyping
For many traits, phenotyping is the limiting
component. Extensive studies of the genetic
control of drought tolerance have not yet
resulted in the deployment of markers for
specific loci and alleles in breeding
programmes. It is difficult to reproduce
seasonal differences in combination with
different genetic backgrounds, and validat-
ing marker–trait associations has been prob-
lematic. However, phenotyping is often
more reliable for some factors affecting root
health, notably tolerance to root disease,
pests and nutrient deficiencies. Reliable
phenotyping leads to more reliable mapping,
usually linked to higher heritability, from
which markers can be readily developed and
deployed.
High-throughput phenotyping facilities
using robotics and image analysis are being
constructed at many research sites (APPF,
2009) but it will be several years before their
impact can be measured. Similar facilities are
already widely used by industry (CropDesign,
2009) to accurately and objectively measure
plant characteristics under a range of
stresses.
226 R. Whitford et al.
Phenotyping systems focusing on clusters
of mega-environments and high-throughput
field-based phenotyping criteria have been
used by CIMMYT and the International Rice
Research Institute (IRRI). When combined
with sampling and data acquisition systems,
phenomics-based protocols for breeding
programmes can be developed. In natural or
controlled environments, drought-tolerance
breeding programmes (CIMMYT, 2009a;
IRRI, 2009) are incorporating techniques
such as remote sensing of plant water status,
canopy chlorophyll content and canopy
temperature.
Genotyping
PCR-based assays have allowed extensive
automation of genotyping, but high marker
development costs and low levels of poly-
morphisms in breeding material have inhib-
ited the use of MAS in many breeding
programmes. Cheap, fast-screening using
single nucleotide polymorphisms (SNPs) has
led to the development of a large SNP detec-
tion industry largely servicing medical geno-
typing but also applicable to crop plants.
Next Generation Sequencing Technologies,
such as Solexa and 454/FLX, have dramati-
cally reduced sequencing costs and SNP
discovery is now possible in species where
other marker systems are poorly developed
such as cowpea, chickpea, pigeonpea and
groundnut (Varshney et al., 2009).
Private companies are using high-
throughput technologies for transgene test-
ing in several model systems.
Example 17: Mendel Biotechnology has over-
expressed 1700 transcription factors in
Arabidopsis and identified transcription factors
related to biomass production, seed yield and a
‘stay-green’ phenotype under drought stress
(Gutterson, 2005). With Monsanto, these genes
have been introduced into important cereal
crops (Monsanto, 2009a). CropDesign has
tested 1400 constructs in rice and identified
genes that enhance seed yield and biomass
(e.g. SYT1 and STZ) (CropDesign, 2009).
Genetic Modification or Transgenic
Technologies
Genetic modification (GM) involves alter-
ation of an organism’s genetic material (DNA
or RNA) involving:
1. Transferring genes between organisms.
2. Moving, deleting, modifying or multiply-
ing genes within an organism.
3. Modifying existing genes.
4. The incorporation of newly constructed
genes into a new organism.
Example 18: GM techniques have been used to
develop male sterility for use in hybrid breeding,
cereals enriched in commercially valuable oils,
proteins and starches as well as resistance to
herbicides such as glyphosate (Roundup®) and
phosphinothricin (Liberty®, Basta®).
Transformation
Transformation of cereal crops such as rice
and barley is possible because of hyperviru-
lent Agrobacterium strains and technical
breakthroughs in the use of cell and plant
selectable markers. It was previously only
successful in dicotyledonous plants.
Example 19: The first, but unsuccessful, trans-
formation of a major crop species was by direct
DNA injection into the shoot apical meristem of
maize seedlings (Coe and Sarkar, 1966). In
1984, the first transgenic tobacco plants (Horsch
et al., 1984) used a natural gene vector system,
the Ti plasmid, of the crown gall-causing bac­­
terium Agrobacterium tumefaciens (Zambryski,
1988).
Another transformation method, ‘biolistics’,
involves firing high-velocity DNA-coated
microprojectiles into plant cells and tissues.
Its disadvantages include higher copy
numbers of unstable transgenes and more
DNA rearrangements.
Both methods have generated commer-
cially grown transgenic plants.
 Biotechnology in Agriculture 227
Plant viral vectors can also be used for
transformation or naked DNA can be directly
taken into protoplasts by treating with poly-
ethylene glycol, divalent cations (either Ca2+
or Mg2+) or electroporation (Holzberg et al.,
2002).
The components of transformation vectors
Transgenes typically contain a gene sequence
encoding a marker used for transgenic plant
cell/tissue selection, a gene of interest and
promoters that drive expression in tissues
or cell layers of interest.
selectable markers  Antibiotic or herbi-
cide-resistant selectable marker genes are
used to identify successful vector incorpor-
ation into transformed cells. Most antibiotic
and herbicide selectable markers inactivate
metabolites (Table 12.2).
trait genes  Trait genes can include novel
gene(s) sequences, which may synthesize a
protein(s) responsible for metabolite
synthesis­or inactivation.
Example 20: Transgenic Golden Rice™ is an
example of modified metabolite biosynthesis.
β-carotene (a pro-vitamin A carotenoid) is
increased using a phytoene synthase from
either daffodil (Narcissus pseudonarcissus) or
maize and a carotene desaturase (CrtI) from
the soil bacterium Erwinia uredovora (Paine et
al., 2005).
The trait gene(s) of interest may be from an
unrelated species or may be a natural or
synthetic allelic variant of an endogenous
gene.
Table 12.2.  Common selectable markers.
Marker
Neomycin phosphotransferase II (nptII)
Hygromycin phosphotransferase (hpt)
5-Enolpyruvylshikimate-3-phosphate (EPSP) synthase
Phosphinothricin acetyltransferase (pat, bar)
Example 21: Superior naturally occurring
HMW-GS alleles (Altpeter et al., 1996) and
synthetic hybrids (Blechl and Anderson, 1996)
have been used to generate transgenic wheat
lines, some of which also possess superior
bread-making qualities (Alvarez et al., 2001;
Barro et al., 2003; Blechl et al., 2007).
Portions of a trait gene can also be used to
induce post-transcriptional gene silencing
(PTGS). PTGS or RNA interference (RNAi) is
the sequence specific degradation of RNA.
Both microRNAs (miRNAs) and small inter-
fering RNAs (siRNAs) are central to RNAi
and have been used to create transgenes
that, upon expression, generate double-
stranded RNA molecules, which are cleaved
by the enzyme Dicer and yield short frag-
ments of about 20 nucleotides. The guide
strand can then base pair with the comple-
mentary mRNA sequence of the trait gene.
Trait gene mRNAs are then cleaved by the
RNAi-induced silencing complex (RISC)
rendering them inactive. Hairpin-induced
RNAi silencing has been demonstrated as an
efficient tool for functional gene character-
ization in several crop species (for example:
Wang et al., 2000; Travella et al., 2006).
For the purpose of PTGS, transgenes can
be constructed to express antisense RNAs
(aRNA), hairpin RNAs (hpRNA) and artifi-
cial precursor miRNAs (amiRNA).
promoters  Promoters are regions of DNA
that facilitate transcription of selectable
marker and trait genes. The most commonly
used promoters in crop transformation
include Ubiquitin (Ubi), Actin (Act1) or a dual
enhanced cauliflower mosaic virus (CaMV)
35S (35Sx2) promoter.
Resistance conferred
Kanamycin
Hygromycin
Glyphosate
Phosphinothricin
228 R. Whitford et al.
Expressed sequence tag (EST) and micro-
array technologies are used to identify
promoters that meet specific expression
requirements for a particular trait gene.
Trait gene-dependent expression require-
ments are particularly important to mini-
mize negative effects associated with trait
gene mis-expression.
Novel transactivation technologies such
as promoter tagging (Johnson et al., 2007)
can be used for promoter identification.
Chemically regulated promoter systems can
also be used to generate transgenics with
tightly regulated gene expression (Moore et
al., 2006).
Cisgenics
Cisgenes derived from the crop plant itself
or from a crossable species (Rommens et al.,
2004; Schouten et al., 2006; Conner et al.,
2007) can counter public concerns about
incorporating prokaryote DNA sequences
into crop species. Cisgenic plants are similar
to those bred by traditional introgression
and translocation breeding; they are faster
to generate than with traditional breeding
and can eliminate problems associated with
linkage drag. In time, cisgenics may be
accepted as an alternative to using prokary-
ote, vector-based systems.
Gene discovery
‘Gene discovery’ is the identification of gene
sequences, and variants, that contribute to a
trait or phenotype. It requires an under-
standing of the complex metabolic and
signal transduction pathways involved in a
trait’s expression. It involves the dissection,
and then manipulation, of fundamental
plant processes to improve crop plants. It
can be either ‘targeted’, starting with defin-
ing a trait of interest and then identifying
the controlling gene sequences, or ‘non-
targeted’, which is quite random.
Targeted gene discovery
map-based cloning  Dense molecular genetic
maps for most crop species (Varshney et al.,
2004) have come from advances in molecu-
lar genetics and automation of the tech-
niques used to identify DNA sequence
variation. The most common assays are for
SSRs or microsatellites and SNPs. They are
abundant and amenable to high-throughput
genotyping.
Example 22: Diversity Array Technology (DArT)
gained prominence because it could profile
genome-wide genetic variation without previous
sequence knowledge (Kilian et al., 2005).
Genetic maps are used for assigning traits of
interest to genomic loci and for map-based
cloning (MBC) where an interesting mutant
phenotype is identified and then genetic fine
mapping occurs using a large number of
recombinant inbred lines (RILs), doubled
haploid, or F2 progeny plants. The genetic
map and marker–trait associations are then
used for chromosome walking and landing,
with the help of large-insert DNA libraries
or physical maps to isolate the gene
(Azhaguvel et al., 2006).
Example 23: MBC is suited to the identification
of QTLs and has been used to identify genes
such as HKT, Sub1A, CBF, ALMT1 and Bot1,
which confer tolerance to salt, submergence,
freezing, aluminium and boron toxicity, respec-
tively (reviewed by Collins et al., 2008).
association mapping – linkage disequilibrium
Association mapping is based on linkage
disequilibrium (LD): the non-random associ­
ation between markers, genes or QTLs in a
population. It takes advantage of events
that created genetic linkage in the relatively
distant past.
Example 24: Large structured breeding popula-
tions have been a valuable resource for associ-
ation mapping and have resulted in the
identification of markers for higher yield and
yield stability in barley (Kraakman et al., 2004),
as well as milling quality and kernal morphology
in wheat (Breseghello and Sorrells, 2006).
 Biotechnology in Agriculture 229
For ‘out-breeding’ species where LD extends
over very short distances, association
mapping is used to identify markers tightly
linked to agronomic traits. This can reduce
the time required for MBC of gene sequences
underlying the trait. This approach is not
suitable where genetic control of the trait is
complex or where there are confounding
factors that may affect trait expression.
Maturity and plant height can strongly
affect drought responses and association
mapping for drought tolerance using a
diverse germplasm collection is likely to only
reveal maturity and height loci.
comparative genomics   Comparison of
genetic maps indicates very good conserva-
tion in the order (colinearity) of molecular
markers and of QTLs for important agro-
nomic traits along the chromosomes within
different families of plants. Comparative
genomics has provided insight into plant
genome evolution: some of the major evolu-
tionary mechanisms during the past 50–70
million years have been unravelled (Salse
and Feuillet, 2007).
Example 25: Recently, genetic and physical
maps have been integrated for plant families
with important domesticated crops, such as the
Poaceae (Devos, 2005), Fabaceae (Zhu et al.,
2005), Roseaceae (Dirlewanger et al., 2004),
Solanaceae (Mueller et al., 2005), Asteraceae
(Chapman et al., 2007) and Brassicaceae
(Schranz et al., 2007).
Evolutionary relationships have been estab-
lished between rice, Brachypodium and
members of the Triticeae. Isolation and
sequencing of large genomic DNA fragments
from different species has highlighted cross-
species gene-order conservation at the sub-
megabase level, that is micro-colinearity (for
example, Chen et al., 1997). In leguminous
species, gene order synteny has been estab-
lished between the model species Medicago
truncatula and Lotus japonicus and other
members of the Papilionoideae, including
soybean, broad bean, chickpea and clovers
(Varshney et al., 2009). Despite no local
micro-colinearity, good colinearity between
grass and legume genomes means that the
number of molecular markers in a targeted
region using restriction fragment length
polymorphism (RFLP) and EST probes may
be increased without additional molecular
markers being needed from the species of
interest (Feuillet and Keller, 2002).
Example 26: Colinearity has been used to iden-
tify gene sequences responsible for disease
resistance (e.g. Lrk, Rph7), development (e.g.
Vrn1, Ppd-H1) and quality (e.g. Ha, Glutenin)
(Salse and Feuillet, 2007). In legumes, compar-
ative mapping has helped to identify nodulation
and nitrogen fixation genes (Zhu et al., 2005).
allele mining  Allele mining is often used to
identify superior haplotypes of gene
sequence variants from wild or mutant
populations.
TILLING (Targeted Induced Local Lesions
IN Genomes) is a common way to discover
SNPs in induced mutant populations. It is a
high-throughput reverse genetic strategy
that is low in cost.
Example 27: TILLING populations have been
created for major crop species including maize,
rice, soybean, barley and wheat (Barkley and
Wang, 2008). Screening for natural variation
using this methodology is termed ‘ecoTILLING’.
The power of TILLING for hexaploid bread
wheat improvement was demonstrated by the
identification of 196 new alleles in the A and B
genome waxy genes (granule bound starch
synthase genes I, GBSS1) from a population of
1152 ethylmethane sulfonate (EMS) induced
mutant plants (Slade et al., 2005). Extending
this to tetraploid pasta wheat identified 50 new
GBSS1 alleles from a population of only 768
individuals (Slade et al., 2005).
Non-targeted gene discovery
est sequencing  Gene sequences and varia-
tions can be directly obtained by randomly
sequencing complementary DNA (cDNA)
clone libraries yielding ESTs, a powerful tool
in the analysis of transcriptomes.
230 R. Whitford et al.
Example 28: Analysis of 580,000 wheat and
370,000 barley ESTs estimates the number of
unique genes to be about 122,000 (~40,000 per
homologous genome) and 50,000 for bread
wheat and barley, respectively (Stein, 2007). This
is comparable to the number of genes (~40,000)
predicted from the complete rice genome
sequence (IRGSP, 2009) and appears to be simi-
lar across many plant species.
Next Generation Sequencing Technologies
(i.e. Solexa and 454/FLX) make it possible to
mine transcriptomes of crop species for
which there is little genomics information.
This is rapidly contributing to the wealth of
EST resources (Varshney et al., 2009) which
are a source of sequence-level genetic vari-
ation and extensively used for functional
molecular marker development. EST-derived
SSR and SNP markers are now routinely
used in trait mapping and MAS. ESTs have
also been used to develop cDNA microarrays
used for transcript profiling (Close et al.,
2004).
whole genome or gene space sequencing
Rice has the smallest cereal genome and was
the first to be fully sequenced (Vij et al.,
2006). The sequence has been used to local-
ize genes in other cereals by comparative
mapping (Bennetzen and Ma, 2003).
The Arabidopsis genome sequence and
both the M. truncatula and the L. japonicus
genome sequences provided similar
resources for the Brassicaceae and
Papilionoideae, respectively (Schranz et al.,
2007; Young and Udvardi, 2009).
Growing evidence about sequence and
gene content variation between, and even
within, species means that species-specific
genomic resources are needed (Wobus and
Sreenivasulu, 2006). ESTs partially fill this
gap.
Ordered physical maps are also being
generated from large insert-libraries (bacterial
artificial chromosomes or BACs) for many of
these crops. Genetically anchored physical
maps are an important resource for MBC
strategies, as they will significantly reduce
the time required for candidate gene isola-
tion. The National Center for Biotechnology
Information (NCBI) database lists genome
sequencing and analysis projects underway
for 128 species (NCBI, 2009) (Table 12.3).
Sequencing for grapevine and soybean has
also now been completed.
Current GM traits
GM crops are currently grown on 125 million
ha in 25 different countries (ISAAA, 2009)
and are largely based around herbicide and
pest resistance lines (Fig. 12.3).
Current pest-resistant GM crops offer
significant value to producers because a large
reduction in the use of pesticides has occurred
and this has lowered production costs and
lessened environmental impact (Knox et al.,
2006). Reduced environmental impact
results from reduced energy consumption
required for pesticide manufacturing, trans-
port and on-farm application, and fewer
chemicals enter the environment. The wide
use of herbicide tolerant crops in many parts
of the world has led to a major expansion of
minimum tillage production systems and
similarly, results in reduced on-farm fuel
consumption.
Many traits related to accommodating
climate change are still undergoing field
evaluation but will appear in commercial
crops over the next few years. Among the
most advanced are several crops with
improved nitrogen-use efficiency such as
those developed by Arcadia Biosciences
(Arcadia, 2009) and drought tolerance where
there have been extensive glasshouse and
field trials (Bahieldin et al., 2005; Wang et
al., 2005; Hu et al., 2006; Nelson et al., 2007;
Rivero et al., 2007).
Table 12.3.  Examples of sequencing projects.
Species Reference
Maize (MGSC, 2009)
Potato (PGSC, 2009)
Papaya (ASGPB, 2009)
Wheat (IWGSC, 2009)
Barley (IBSC, 2009)
Tomato (SGN, 2009)
Sorghum (DOE-JGI, 2009)
 Biotechnology in Agriculture 231

40

35
Commercialized GM varieties (%)
30

25

20

15

10

0
Herbicide Pest Stacked Product Other
tolerance resistance HT & PR quality
(HT) (PR)
Trait
Fig. 12.3.  United States Department of Agriculture (USDA)-approved commercialized GM varieties as of
May 2007, by trait (based on data from Oborne, 2009).

On a precautionary note, glasshouse Example 29: Monsanto has demonstrated that

performance and even some field trial results there is a direct relationship between biotech-
may not necessarily provide a reliable nology research and development (R&D) spend-
assessment of the value of these genetic ing and increases in gross profit (Monsanto,
modifications to commercial performance in 2009b). By increasing R&D spending by 9% per
the field over multiple seasons and year since 2001, Monsanto has increased its
environments (Passioura, 2006). seed business gross profit by 24% a year
(Monsanto, 2009b). Other multinational
companies have made large investments in
Capacity building people, infrastructure and germplasm needed
to deliver biotechnology. Germplasm acquired
Significant international capacity building during DuPont’s amalgamation with Pioneer is
has occurred in agricultural biotechnology valued at US$975 million (SEC, 2008) among
since it was identified that biotechnology its other intangible assets. In its last annual
could improve yield in food crops. This report, as a result of its ongoing investment in
capacity has comprised not only infrastruc- agricultural biotechnology, DuPont expected
ture and research capability but has included that in 2009 its agriculture and nutrition division
a steady building of ‘intangible’ assets such would introduce 26 new soybean varieties and
as intellectual property (IP) portfolios and 96 new maize hybrids (SEC, 2008).
germplasm. Capacity has been built to
develop genetically modified organisms In the public sector, significant agricultural
(GMOs) and also to refine techniques used biotechnology capacity has been developed in
in conventional plant breeding. many countries within universities, govern-
In the private sector, the promise of large ment agricultural departments, special
returns from agricultural biotechnology has research centres and so on. Various centres
led to several large multinational seed and programmes have also been established
companies investing in significant infra- to assist the development of technologies for
structure and research capacity (Table 12.4). the developing world.
232 R. Whitford et al.
Table 12.4.  Estimated 2006 R&D expenditures of relevance to
biotechnology by leading companies in each application (based on data from
Oborne, 2009).
Company (country)
Syngenta (Switzerland)
Monsanto (USA)
Bayer CropScience (Germany)a
DuPont Pioneer (USA)
BASF (Germany)
LimaGrain (France)
KWS SAAT (Germany)
Dow Agrosciences (USA)
Total
a Bayer figures are for 2007.
Example 30: The Consultative Group on
International Agricultural Research (CGIAR)
system alone provides over US$500 million to
8096 staff across 15 research centres and four
major research programmes – the ‘Challenge
Programs’ (CGIAR, 2007). Of this, US$19
million was invested in hard infrastructure, the
balance on intellectual capacity.
It is difficult to estimate the actual
amount invested by the public sector in
agricultural biotechnology but most
developed countries support large research
efforts. In the 2008 round of funding under
the National Science Foundation’s Plant
Genome Program, US$60 million was
awarded (NSF, 2008). Similar programmes
exist in most developed countries and total
investment from the public sector in plant
biotechnology research will be in the
hundreds of millions of dollars.
Technology Access
The patent system grants monopoly rights
to patent owners so that they can exclude
others from practising patented technologies
for a period of time. The quid pro quo is that
society is afforded free access to those
inventions upon the expiry of the patent.
Large international companies have
scrambled to gain market monopoly returns
by assembling large patent portfolios. These
Biotech R&D expenditure
(US$ millions)
  510
  470
  310
  190
  170
   85
   65
   55
1855
portfolios not only include genetic tech­
nologies per se, but also so-called ‘enabling’
technologies such as trans­formation methods,
selectable markers, promoters and so on. In
this area, 71% of the IP related to these
technologies is held by the private sector.
Monsanto and DuPont together hold 27% of
the agricultural biotechnology patents (Graff
et al., 2003). These large and complex IP
portfolios, and the use of overlapping groups
of patents, or patent ‘thickets’, have been
developed as a ‘barrier to entry’ for
competitors. The monopoly positions have
not only been built by developing IP within
these companies, but also by the strategic
acquisition of smaller companies with small,
but valuable, IP portfolios.
While this strategy appears to have
delivered above-average financial returns for
those companies, it may have had a negative
effect on the ability of publicly funded
scientists to conduct research using the
latest ‘state of the art’ (Fig. 12.4). Some large
companies have been hesitant to provide
licences to their commercial know-how on
the basis that such licences may erode their
above average returns.
It has now become necessary for research
organizations to conduct extensive ‘freedom
to operate’ searches and then if possible to
obtain the necessary licences so that they do
not infringe the patent rights of others.
Table 12.5 shows the IP rights attached to
various elements of the famous ‘Golden
Rice™’ product.
 Biotechnology in Agriculture 233

followed very limited experimental use

Obtain licence exemptions in the USA and more generous
exemptions in Europe. Such exemptions
vary widely in scope and there is little
or
harmonization across jurisdictions.

Work around solutions

Infringe deliberately
(or unknowingly)
Avoid using technologies
Fig. 12.4.  Intellectual property (IP) options for
scientists.
Some countries have therefore legislated
research exemptions so that scientists may
access and use patented technologies for
research. In 2005, the Australian Advisory
Council on Intellectual Property recom­
mended that the Australia Patent Act be
modified to allow restricted experimental
use (ACIP, 2005). This recommendation
Delivery Pathways and Processes
MAS
MAS has enhanced conventional breeding
methods by providing greater flexibility and
new selection strategies than were previously
possible. The delivery pathway for
bio­technology has been facilitated by
training of a new generation of plant
breeders who have a thorough knowledge of
molecular biology, genetics and heritability.
Some of the key factors influencing marker
application are listed in Table 12.6.
GM
From 1995 a new industry rapidly developed
to generate GM plants, but there have only
been a small number of successful exploit­
ations. Large firms have commercialized

Table 12.5.  Material Transfer Agreements (MTAs), licences, documents and agreements required for
‘Golden Rice™’ (modified from Kryder et al., 2000).
Component Source
Germplasm Rice lines used for transformation Taipei 309 from IRRI
Vector pGEM4 Promega
pBluescriptKS Stratagene
pCIB900 Ciba-Geigy (now Syngenta)
pKSP-1 Tom Okita, Washington State University
pUCET4 N. Misawa, Kirin Brewery Co.
pYPIET4 Clontech (now marketed through Life
Sciences)
Promoters CaMV 35S promoter Monsanto
GT-1 promoter Tom Okita, Washington State University
Terminators CaMV 35S terminator Monsanto
Selectable marker AphIV gene, hygromycin Ciba-Geigy (now Syngenta)
phosphotransferase
Expression enhancement Pea Rubisco transit peptide N. Misawa, Kirin Brewery Co.
pPZP100 Pal Malinga, Rutgers University
Transformation process Electroporation apparatus Bio-Rad
Microprojectile bombardment Bio-Rad
apparatus
Biolistic transformation DuPont
Trait gene Crt1 gene, phytoene desaturase N. Misawa, Kirin Brewery Co.
234 R. Whitford et al.

Table 12.6.  Factors related to effective delivery of marker technologies.

Factor
Direct involvement of breeders in Molecular groups should act in a support capacity, challenging
defining targets and
germplasm
Use cultivated germplasm pool
first
Access suitable staff
‘Outsource’ marker work
Use ‘technology champions’
Establish new generation of
breeders
Comments
breeders by questioning their methods and breeding strategies
For many crop species the level of understanding of variation and
the germplasm base is still poor and introgression of useful alleles
from landraces and wild relatives remains slow
It remains difficult to attract high-quality students and staff to
breeding-related programmes and to attract staff trained in
molecular techniques to breeding stations that are often in remote
locations
High quality and cost-effective service labs are available but many
still believe that marker development and application is still a
research activity and is best carried out in-house
Success in marker application in the public sector is often driven by
a few individuals who had the energy to drive aggressive, and
often risky, new breeding strategies
Major advances in marker application are often driven by more
recently trained breeders

GM technologies mainly focusing on single biotechnology means that access must be

gene events conferring either herbicide or
pesticide resistance, selected because they
are of high commercial value, quick to
market and synergistic with chemical
businesses often owned by the same
companies. Many outcomes of more difficult
projects, such as conferring drought
tolerance, more efficient use of fertilizer,
resistance to salinity and so on, have yet to
be commercialized. Much of the gene
discovery work in these areas is occurring in
the public sector where public funding is
able to overcome the market failure issues
that arise from the extended time needed to
solve these difficult problems.
The delivery pathway for GM technologies
is somewhat more complex than delivering
technologies via conventional breeding.
Identifying genes responsible for traits of
interest is in itself a long and costly process.
Many years of expensive research can elapse
before a trait–gene relationship is discovered
and the gene is isolated. In the case of the
boron tolerance gene, Bot1, at least 4 years
of work was required before the gene was
discovered and patented (Sutton et al.,
2007).
After gene discovery, suitable plants must
be transformed with the gene of interest.
The complex IP landscape in agricultural
sought for the enabling technologies that
are used to create transgenic plants because,
as already mentioned, many of the enabling
technologies are patented. Generating GM
events means that vectors must be
constructed, often also using elements such
as promoters that are also patented (Fig.
12.5).
Transgenic plants are then subjected to
years of testing in glasshouses under
controlled and contained environments.
Monsanto’s ‘product pipeline’ (see Table
12.7) describes just a 25% chance of
successfully delivering a technology once
that initial discovery work has been done.
Plants are then tested under field
conditions at many sites, and usually over
several years, so that the full extent of the
plant improvements are understood and
validated. While initial work often occurs in
‘model’ plants that are easily transformable,
adapted germplasm must be selected that is
suitable for the target environment and
which must also be suitable for
transformation or, if not, then capable of
being ‘backcrossed’ with material that has
been transformed.
Large multinational firms have resources
and expertise, access to complex patent
thickets, extensive access to germplasm and
 Biotechnology in Agriculture 235

can range from several months to well over a

Gene discovery
Access to IP
Construct vector
Transform
Validate in glasshouse
Validate in field
Advanced development
Pre-launch
Fig. 12.5.  Technology development.
well-developed ‘pipelines’ for delivering
genetic technologies. It is for these reasons
that the only practical way of delivering new
GM technologies is for public sector organ-
izations to partner with such firms.
Regulation
GM organisms are subject to tight regulatory
approvals in countries where they are
developed and grown. These regulations
allow GM research only in suitably approved
containment facilities and by organizations
and staff who have the appropriate
qualifications and experience.
For GM crops, field evaluation is an
essential component of the development
and delivery process. Special approvals are
required for conducting such trials. In some
countries, the approval process is relatively
straightforward although the approval times
year and appear to be increasing. This means
that GM lines being evaluated are often not
the latest, or most suitable, for analysing
trait expression. In some jurisdictions,
notably in some European countries, the
costs of running a GM field trial are
prohibitive and trials are frequently
destroyed by anti-GM lobby groups.
Full commercial release of a GM crop will
require full regulatory approval both in the
country of production and in all the
jurisdictions where the GM product may be
imported. Since 1995, the time to obtain
regulatory approval has increased markedly
in the USA and indeed no new crop obtained
approval in the USA in the 5 years from 2000
(Jaffe, 2005).
Commercial seed companies have rarely
provided estimates of the costs to deregulate
a biotechnology crop. However, the costs are
‘many times higher than the regulatory costs
for a non-GM plant variety, which range
from US$5000 to US$11,000’ (Oborne,
2009). Table 12.8 provides a summary of
some of the cost estimates.
The international regulatory require­
ments are derived from the 1992 Rio
Declaration on Environment and Develop­
ment, Principle 15 ‘where there are threats
of serious or irreversible damage, lack of
scientific certainty shall not be used as a
reason for postponing cost-effective
measures to prevent environmental
degradation’ (UNEP, 1992). This requires
extensive evaluation and testing of any GM
crop.

Table 12.7.  Monsanto’s product pipeline (modified from Monsanto, 2008).

Early product Advanced

Proof of concept development development Pre-launch
Key activities Gene optimization Large-scale Trait integration Regulatory
Crop transformation   transformation Expanded field   submission
Field evaluation Trait development   trials Seed bulk-up
Pre-regulatory data Regulatory data Pre-marketing
generation
Average duration 12–24 months 12–24 months 12–24 months 12–36 months
Average 25% 50% 75% 90%
  probability of
  success
236 R. Whitford et al.
Table 12.8. Costs to deregulate a GM crop.
Cost estimate (US$)
40–50 million
6–15 million for a herbicide-tolerant maize
‘Up to 13.5 million’
The requirements for international
movement of a GM product are outlined in
the Cartagena Protocol on Biosafety (CBD,
2007) and ‘Contribute to ensuring an
adequate level of protection in the field of
the safe transfer, handling and use of living
modified organisms …’. This agreement
prescribes a process for the transport of GM
products between countries known as the
Advanced Informed Agreement Procedure,
which requires the exporter to provide
detailed information to the importing
country. The importing country must have a
competent national authority, which can
acknowledge receipt of information,
authorize shipment or give reasons for
rejection. This procedure only applies to the
first movement of the GM product and is
not required if the GM plant is in transit, for
contained use or will go directly into food or
feed and will be rendered non-viable.
Governments are also able to notify the
Biosafety Clearing House of approval and
provide detailed information supporting
this (CBD, 2009). This provides a central
repository of regulatory and evaluation
information on GM crops and products.
As with regulations for GM research, field
evaluation and commercial release, the regu-
lations covering the acceptance and use of
GM foods vary greatly between countries
with the most stringent in the European
Union. An extensive literature has been
developed around the safety assessment of
GM foods (FAO/WHO, 2000). The complex-
ities associated with both the development
and the release of GM crops has meant that
most commercially grown GM crops have
been released by the private sector. However,
in some countries, notably China, strong
public sector and government support for
GM crops has led to the development and
release of several GM crops.
Source
Anecdotal from multinational companies
Kalaitzandonakes et al. (2006)
Organisation for Economic Co-operation and
Development (OECD) report (Oborne, 2009)
Conclusions
Biotechnology provides a range of new tools
and techniques that can provide increased
flexibility and efficiency to plant breeders.
Some of the most promising targets are
described in Table 12.9.
Despite climate change, breeders will be
able to respond more rapidly to the require-
ments of cropping systems. Improvements
in conventional breeding are already being
realized by many programmes through the
application of molecular markers, the use of
doubled haploids and a greater understand-
ing of genetic diversity available for plant
improvement (see Reynolds et al., Chapter 5;
Braun et al., Chapter 7, this volume). Through
climate change the environments being
targeted by breeders will also shift resulting
in changes in the disease and pest spectrum
being faced by farmers and in a direct reduc-
tion in the stability of yield through adverse
climate, such as increased frequency of
drought.
In addition to the direct impact of climate
change, the community is also expecting
agriculture to address production inefficien-
cies, such as high fuel, fertilizer, pesticide
and fungicide applications. In many cases,
these represent new targets for breeders but
they can be rapidly addressed through the
application of new molecular techniques.
Genetic engineering or modification
offers a means to accelerate plant improve-
ment and to access diversity not available
within the crossable gene pool for many crop
species. Where farmers have access to GM
technology, extremely rapid adoption has
resulted in clear benefits to both the
pro­ducer and the environment. However,
limited consumer acceptance of GM, partic-
ularly in Europe, has limited access to the
technology and led to high regulatory costs.
Table 12.9. Towards 2030: the most promising biotech applications.

Climate change-related problem
Plants will be exposed to greater
extremes in conditions
Water supply may become limited
or more variable
Application Recent developments
Flowering time Gene sequences have been identified that
determine flowering time for many crops.
Rapid ‘fine tuning’ of crop phenology and life
cycle duration can maximize yield under
diverse climatic conditions
Drought tolerance and Omic analyses have enabled better
yield under water- understanding of regulatory networks
limited conditions controlling plant responses to limited water
supply. Functional genomics has also enabled
the identification of genes regulating drought
responses
Methods to ameliorate effects of climate change
Match plant development to availability of
radiation, water and nutrient resources.
Minimize exposure to climatic extremes at
critical developmental stages (Craufurd and
Wheeler, 2009)
Tailor molecular drought response regulators to
engineer water-use efficient and drought-
tolerant crops. Modify drought tolerance
according to the time of onset of water
constraints

Higher temperatures are likely
Increasing soil salination from
coastal salt water inundation,
reduced rainfall and increased
irrigation
Fertilizer use and production emits
1.2% of the world’s greenhouse
gases (Wood and Cowie, 2004);
N fertilizer production consumes
ten times more energy than
other fertilizers (Lal, 2004)
Disease infection and pest
infestations may increase
Biotechnology in Agriculture
Heat tolerance Yields increase with temperature up to a critical Identify physiological mechanisms and
threshold and then decline sharply. Climate associated molecular markers for application
change is predicted to increase the likelihood in crop breeding programmes. Advances in
of heat stress in many cropping regions stress/trait dissection and rapid phenotyping
will enhance the understanding of the
physiological and genetic bases of heat
tolerance
Salinity tolerance Identification of gene sequences and Select for salt tolerance using direct phenotyping
quantitative trait loci controlling Na+ or molecular markers. Engineer cell-specific
exclusion and tissue tolerance Na+ exclusion using identified gene sequences
as a more efficient strategy for salt-tolerant
crop development (Møller et al., 2009)
Nutrient-use Crops only recover around 50% of N supplied Transfer N-use efficiency gene sequences to
efficiency (Eickhout et al., 2006). Identification of gene other major crop species, including maize and
sequences controlling N-use efficiency has wheat, as a major target for commercial plant
led to more fertilizer-efficient rice (Shrawat et breeding (Arcadia, 2009)
al., 2008)
Disease/pest The dependence of pest and disease dynamics Manipulate levels of existing anti-pathogen or
resistance upon prevailing temperature and rainfall pest compounds (Delaunois et al., 2009;
profiles makes future pest and disease Hexima, 2009) or, through using novel
outbreaks notoriously difficult to predict biotechnology strategies (Nolke et al., 2004),
(Gregory et al., 2009). Breeders may not be identify novel pathogens and monitoring

237
able to keep pace with changes pathogen spread (Park, 2008)
238 R. Whitford et al.
The high costs have virtually eliminated the
public sector’s ability to deploy GM technol-
ogies and have restricted the types of traits
and the crops in use. However, there are
signs in several countries that community
attitudes to this technology are changing,
particularly with respect to the use of GM
crops to improve tolerance to environmental
stresses.
The combination of new methods in plant
breeding, including MAS as well as the
opportunities provided by GM crops,
increase both the speed and the flexibility of
crop improvement. However, relatively few
breeding programmes have had the regula-
tory framework, skills, background informa-
tion and technology access needed to deploy
these methods. These limitations remain the
major impediment to the widespread use of
biotechnology and they will only be
addressed through strong international
collaboration and capacity building.
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13
GIS and Crop Simulation
Modelling Applications in
Climate Change Research

David Hodson and Jeffrey White

Abstract
The challenges that climate change presents to humanity require an unprecedented ability to predict
the responses of crops to environment and management. Geographic information systems (GIS) and
crop simulation models are two powerful and highly complementary tools that are increasingly used
for such predictive analyses. The role of both technologies in predicting future situations centres
around extrapolation. For GIS, extrapolation from the past based on correlation in a very loose sense
plays an important role. For crop models, extrapolation based on how known processes respond to
factors of interest (i.e. simulation) is a key factor. GIS and crop models can be integrated, providing
predictions that combine the spatial perspective of GIS with the stronger representation of temporal
processes of simulation models. This chapter reviews the use of these two tools for predicting impacts
of climate change and examining options for adaptation. Increasingly, downscaled outputs from a
range of global general circulation models under differing future scenarios are used as key inputs for
both tools. Examples are given for major food crops and key agricultural zones, with a bias towards
tropical and subtropical regions. Consideration is also given to factors limiting efficient application of
the tools to climate change research. Both technologies will see increasing use in climate change
research and in applications of research in decision making. Credible studies of crop responses to
climate involve dealing with large sets of data and potentially millions of simulations, especially if
adaptation is considered. While the computational challenges are daunting, the greater challenge is
how to devise efficient protocols for selecting the most meaningful scenarios, interpreting the results
and summarizing outputs for decision makers.

Introduction The inherently spatial aspects of climate

The challenges that climate change presents
humanity require an unprecedented ability
to predict the responses of crops to environ-
ment and management. Geographic infor-
mation systems (GIS) and crop simulation
models are two powerful and highly comple-
mentary tools that are increasingly used for
such predictive analyses. Most notably, the
portions of the Fourth Assessment Report
(FAR) of the Intergovernmental Panel on
Climate Change (IPCC) (Easterling et al.,
2007) that dealt with agriculture made
extensive use of predictions from crop
models and in many cases, the regional
assessments that they summarized also
involved GIS (e.g. Thornton et al., 2006).
and climate change make them readily amen-
able for incorporation into a GIS-based
analysis­ system. It is becoming ever more
apparent that climatic changes are occurring
non-uniformly across regions or agro­
ecosystems. GIS provides a useful tool to
capture this spatial heterogeneity and
provides powerful ways in which to visualize
and communicate the actual or potential
changes that are occurring. A GIS-based
framework has been the fundamental element
of several major assessments of the potential
impact of climate change on agriculture (e.g.
Tubiello et al., 2000; Fischer et al., 2002; Parry
et al., 2004).
The flexibility of GIS-based analysis
systems to handle differing scenarios in

© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 245
246 D. Hodson and J. White
a rapid and efficient manner is another
important factor. The suite of advanced
global general circulation models (GCMs)
that inform major assessments such as those
of the IPCC (e.g. Solomon et al., 2007), and
the accompanying emission scenarios devel-
oped for the IPCC assessments (IPCC, 2000)
form the basis of many climate change
assessments (e.g. Parry et al., 2004; Lobell et
al., 2008). Increasingly, the outputs of the
GCMs under differing emissions scenarios
are available in data formats suitable for
direct use in GIS-based systems (e.g. the
WorldClim data set (2009) see http://www.
worldclim.org/futdown.htm). The avail-
ability of multiple GCM outputs, coupled to
GIS-based systems, has permitted increas-
ing opportunities for analysis of spatial
convergence or divergence of GCM outputs
at global or regional scales (Neelin et al.,
2006; Lobell et al., 2008).
Crop models integrate available informa-
tion on plant ecophysiology, soil chemistry,
agroclimatology and related fields, and simu-
late key processes thought to determine crop
performance in a given environment. For
climate change assessments, yield responses
for major crops are derived mainly from
applications of crop growth simulation
models coupled to global or regional climate
change models and run under a range of
emission scenarios. Coupling mainstream
crop simulation models such as ceres and
apsim to a suite of five to ten widely accepted
advanced GCMs, for example the Hadley
Centre’s HadCM3 or CSIRO’s MK3, and
evaluation under the standard range of IPCC
emission scenarios has been a common
approach (e.g. Defra, 2004, 2005).
Meta-analysis of several such global simu-
lation studies as reported by the IPCC Third
Assessment Report (TAR) (IPCC, 2001) and
supported by the IPCC FAR (2007) is, not
surprisingly, revealing differences between
crops and regions, but several global trends
are apparent. With global warming, many
studies are now indicating an increasing
polarization between the high-latitude
developed countries and the low-latitude
developing regions (e.g. Parry et al., 2004).
Taking a major cereal crop like wheat as
example, slight increases in yields at mid- to
high latitudes are predicted if moderate
mean temperature increases (1–3°C) occur.
However, further warming, even in temper-
ate regions, causes yields to decrease. In
subtropical and tropical regions, wheat is
often already near its limit of maximum
temperature tolerance, so small temperature
increases (1–2°C) reduce yield. Outputs from
such simulation studies are providing useful
information to inform future decision-
making processes, although several uncer-
tainties still remain, for example the extent
and role of CO2 fertilization effects (Long et
al., 2006; Tubiello et al., 2007).
Crop simulation models and GIS are vital
tools in predicting the impacts of climate
change in agricultural systems. The two tools
are complementary and the role of both
technologies in predicting future situations
centres around extrapolation. For GIS,
extrapolation from the past based on correl-
ation in a very loose sense plays an import-
ant role. For crop models, extrapolation
based on how known processes respond to
factors of interest (i.e. simulation) is a key
factor, with the models often supported by
GIS.
This chapter reviews the use of these two
tools for predicting impacts of climate
change and examining options for adapta-
tion. GIS and crop models can be integrated,
providing predictions that combine the
spatial perspective of GIS with the stronger
representation of temporal processes of
simulation models.
Examples are given for major food crops
and key agricultural zones, with a bias
towards tropical and subtropical regions.
Consideration is also given to factors limit-
ing efficient application of the tools to
climate change research. The focus is exclu-
sively on climate change and increased CO2,
but principles are similar for O3, N depos-
ition and other factors, which are often
included within global change.
Role and Applications of GIS
A GIS represents a computer-based system
for the management of geographically refer-
enced data – that is, data that can be
 GIS and Crop Simulation Modelling Applications 247

connected to a specific location on the Earth Globally, GIS is applied to disciplines

and mapped. Many definitions of a GIS exist,
but one used by a major GIS software
company ESRI (Redlands, California) has
relevance in the context of this chapter:
GIS is a computer technology that uses a
geographic information system as an analytic
framework for managing and integrating
data; solving a problem; or understanding a
past, present, or future situation. GIS is,
therefore, about modelling and mapping the
world for better decision making.
Common tasks within a GIS include the input,
storage, manipulation, analysis and display
(often in the form of maps or graphs) of geo-
referenced data. Mapping is a key output of
any GIS, but it is certainly not the only func-
tionality. Common data inputs include data
in either vector or raster (gridded) formats.
The latter are particularly useful for the repre-
sentation of continuous data (e.g. climatic
variables) and cell-by-cell modelling.
ranging from managing utility networks to
health, archaeology and ecology. Increasingly,
it is a common component of climate change
assessments. The geographic aspect of GIS
makes it an interesting option for applica-
tion to agricultural problems and priority
setting because so many of the environ-
mental and socio-economic factors that
impact agriculture or agricultural research
vary greatly over regions (e.g. Benson, 1996).
Typical examples would include rainfall
patterns, soil variability, disease and pest
distribution, market locations, crop distri-
butions, land-use patterns and human
demographics (Table 13.1).
Historically, GIS has seen widespread use
for delineation of suitability zones and agro-
ecological zonation (e.g. Hartkamp et al.,
2001; Setimela et al., 2005). The ability to
combine multi-thematic data based on
common geography has been an extremely
powerful tool. Common approaches to general

Table 13.1.  Examples of typical application themes for GIS/spatial technologies.

Thematic area
Rainfall/climate patterns
Soil variability
Disease and pest distribution Actual distributions and climatic
Market locations/accessibility Accessibility surfaces based on least
Crop distributions
Land-use patterns
Human demographics
Abiotic stresses
Identification of wild species
collection sites/suitability
zones
Crop suitability zones and
agroecological zonation
Comment Example reference
Interpolated raster (gridded) surfaces Hijmans et al. (2005)
derived from meteorological station
data
Spatial variation of major soil types Batjes (2009)
and derived soil properties
Sutherst et al. (1996), Sutherst
suitability zones and Maywald (2005)
Uchida and Nelson (2009)
cost distance travel times
Spatial allocation of reported Leff et al. (2004), You et al. (2009)
agricultural census data into most
likely areas using land use and
suitability
Satellite-derived land-cover estimates Bicheron et al. (2006)
on varying spatial and temporal
scales
Gridded surfaces of human Budhendra et al. (2002), CIESIN,
population density Columbia University and CIAT
(2005)
Modelled spatial distributions of key Thornton et al. (2006), Hodson
stresses, e.g. drought, heat and White (2007)
Actual distributions and modelled Jarvis et al. (2003)
ecological niches for important wild
relatives of crop species
Climate, soil and landform-based Hartkamp et al. (2001), Setimela
agroecological zones for major et al. (2005)
crops
248 D. Hodson and J. White
crop suitability mapping have included the
geographical overlay and intersection of key
factors such as optimal temperature and
moisture ranges, soil types and topographic
features. GIS is perfectly suited for undertak-
ing such analysis.
Similar approaches have been undertaken
to determine environmental niches in which
wild relatives of crops are most likely to
occur. The example of the FloraMap™ and
Homologue™ tools developed at Centro
Internacional de Agricultura Tropical (CIAT)
(Jones and Gladkov, 2001; Jones et al., 2005)
typifies this approach. Climatic and environ-
mental conditions existing at known collec-
tion sites are used to derive a probabilistic
determination of extrapolated similarity
zones. This extrapolation, often based on
relatively sparse input data, has been used
to determine priority zones for future collec-
tion efforts of valuable genetic resources or
in situ conservation (Jarvis et al., 2003).
Both FloraMap™ and Homologue™
output climate similarity probability maps
in GIS data formats.
Location-based climatic factors have also
formed the basis of zonations for targeting
germplasm of major food crops. Mega-
environment classifications have been
defined by the International Maize and
Wheat Improvement Center (CIMMYT) for
both maize and wheat to delimit broadly
homogenous global production zones (Braun
et al., Chapter 7, this volume). They have
been used to assist with priority setting and
targeting of germplasm (Setimela et al.,
2005; Hodson and White, 2007). For wheat,
the extensive network of international
wheat trials was the foundation for mapping
mega-environments. GIS tools permitted
the extraction of climatic and edaphic data
from the trial sites and subsequent cluster
analysis determined quantitative limits for
separation of the major global environments
(Hodson and White, 2007). For maize a
similar approach was taken, with the climatic
and edaphic data extracted from trial site
locations being fundamental to the analysis.
In the case of maize, germplasm perform-
ance data from the trials was combined with
the environmental data and entered into a
genotype-by-environment (G × E) analysis.
The resulting mega-environment criteria
reflected the major drivers of G × E (Setimela
et al., 2005). For both maize and wheat, the
final mega-environments had clearly defined
quantitative climatic parameters as their
foundation, hence mapping of the spatial
distributions was a simple task.
Climate-based mapping of potential pest
and disease probability occurrence zones is
also relevant to the scope of this review. This
has been undertaken using very similar
approaches to those described for wild rela-
tives and crops. The climex model devel-
oped by Sutherst and Maywald (1991)
combines climatic suitability (a growth
index) with stress indices to produce an
overall index of suitability for a given species
at a specific location. Conditions under
which known distributions are found are
used to infer potential distributions in new
areas. The model has been successfully
applied to a range of pest and disease species
(e.g. Sutherst et al., 1996; Sutherst and
Maywald, 2005). As in the case of
FloraMap™, model outputs are displayed
in map form and exported in GIS data
formats.
Abiotic stresses, such as drought, have
also been assessed using GIS-based analyti-
cal approaches. Again climate is a key driver
and GIS captures the spatial variation that is
essential to interpretation in an agricultural
context. One example of an approach to
drought modelling was the ‘failed season’
approach described by Jones (see Thornton
et al., 2006) and applied to Africa. A water
balance model was used, coupled to derived
daily climate data for 30 years obtained from
the MarkSim™ weather generator (Jones
and Thornton, 2000). A season was deter-
mined to fail if an insufficient water balance
was maintained throughout the growing
season of a typical crop. The final outputs
were mapped as a probability of failed
seasons at a 30 arc sec (approximately 1 km2
grid) for the entire African continent.
These examples illustrate how GIS has
been the key technology applied to a range
of differing agroecological themes. Spatial
integration of multi-thematic data sets was
a common element, but so too was use of
climate data. This pivotal role of GIS in
 GIS and Crop Simulation Modelling Applications 249

agroclimatic­analysis is relevant whether the
analysis is based on current or historical
climate data or predicted future climate
data. The increasing availability of outputs
from a range of GCMs under varying emis-
sion scenarios is permitting a range of
GIS-based assessments of the potential
characteristics of future crop production
zones, and associated abiotic and biotic
stresses. Several illustrative case studies will
be described in succeeding sections that
build upon the examples and themes already
outlined.
Role and Applications of Crop
Simulation Models
Crop simulation models use quantitative
descriptions of ecophysiological processes to
predict plant growth and development as
influenced by environmental conditions and
crop management that are specified for the
model as input data (Table 13.2). Many
models developed by a single researcher or
laboratory are used for a single purpose and
have a short life. Others evolve over time
and are similar to modern software pack-
ages. Among the longer lived models that
have seen widespread use in climate change
research are apsim (Keating et al., 2003), the
Cropping Systems Model (csm) series (Jones
et al., 2003; Hoogenboom et al., 2004),
CropSyst (Stockle et al., 2003) and epic
(Meinardus et al., 1998).
The simplest models estimate daily
growth through conversion factors for inter-
cepted solar radiation to biomass, whereas
complex models may simulate growth at a
timescale of minutes and include routines to
simulate key biochemical pathways of photo-
synthesis. Hay and Porter (2006) provide a
general review of the physiological processes
described in models, and Tsuji et al. (1998)
describe multiple aspects of models, includ-
ing soil and weather processes and example
applications.
A typical model simulates assimilate
production by estimating gross photosyn-
thesis and then reducing the assimilate pool
through respiration and senescence. The
resulting net pool is then allocated to

Table 13.2. Examples of data inputs required for a typical crop model that runs with daily time steps.
Variable Comments
Daily weather
Maximum and minimum air Affect almost all plant and atmospheric processes and are also used
temperatures to estimate soil temperatures
Solar radiation Key for establishing potentials for photosynthesis and
evapotranspiration. Data are often either unavailable or inaccurate
Precipitation Affects moisture levels in the soil profile and runoff
Dewpoint or vapour pressure Affects potential evapotranspiration. Average relative humidity is often
deficit reported but is a poor indicator of evaporative demand because of
confounding with temperature
Wind speed Affects potential evapotranspiration
Soil properties
Albedo Reflectivity of soil to solar radiation. Affects soil temperature and
evaporation
Runoff characteristics Used to estimate what fraction of precipitation is lost to runoff
Infiltration characteristics Used to estimate how moisture enters the profile, is distributed
through soil layers, or drains out of the profile
Initial water and nutrient levels Establishes soil conditions for germination and subsequent growth.
Preferably determined by soil horizons to the maximum depth of
root development
Crop management
Sowing rate Used to estimate initial stand of plants
Row spacing Used to estimate light interception by crop canopy
Fertilization Type, amount and date of application for any fertilizers
250 D. Hodson and J. White
different plant organs through partitioning
rules. The rules assign priority to rapidly
growing tissues such as leaves, with onset of
reproductive growth representing a key
developmental switch. Priorities also shift in
order to satisfy the crop demand for water
and nutrients. If supplies are limiting, more
assimilate is allocated to root growth in order
to increase extraction from the soil. Thus,
under water or nutrient deficits, root growth
may be favoured over leaf, stem or reproduc-
tive growth. Furthermore, nutrients may be
mobilized from inactive tissues (e.g. older
leaves) to organs with high demand.
The timing of key developmental stages
such as seedling emergence, end of main
stem leaf appearance, anthesis and physio-
logical maturity are simulated using proced-
ures that are analogous to the accumulation
of growing degree days (heat units). As
required for a given crop, however, the
procedures may consider vernalization and
photoperiod responses. Models for simulat-
ing root and tuber, forage and bioenergy
crops are similar to those for seed and grain
crops, but allocate assimilates to vegetative
storage organs (Singh et al., 1998).
Water and nutrient budgets are usually
modelled both for the plants and for the soil,
requiring descriptions of root growth
through the soil as well as the soil and atmos-
pheric processes that affect water and nutri-
ent dynamics.
Temperature responses
The main effects of temperature are modelled
on assimilate production, phenology, soil
processes and evapotranspiration. Relatively
few models explicitly consider high tempera-
ture stresses causing abortion of reproductive
structures or irreversible damage to vegeta-
tive organs. For models that estimate daily
growth through a radiation use efficiency
(RUE) approach, the potential RUE is adjusted
by a simple temperature function. In the
version of the ceres models implemented in
the csm series, these temperature functions
weight the daily maximum three times more
than the minimum, on the assumption that
daytime temperatures influence growth more
than night-time temperatures. More complex
models such as those using the Farquhar
model may involve multiple temperature
responses that are evaluated at scales of
minutes, and the parameters are determined
by measuring component physiological
processes.
The occurrence of stages such as flower-
ing and maturity is hastened by tempera-
ture, but interactions with vernalization (a
requirement for cold temperatures prior to
flowering) and day length can override the
basic effect of temperature on development.
Physical and chemical processes affecting
water and nutrient availability also respond
to temperature. The net result is that the basic
temperature responses described by models
are more complex than one might expect.
Response to CO2
In RUE-based models, the main effect of CO2
is through a factor that scales RUE down-
wards or upwards, a key distinction being
whether the crop has a C3 or C4 photosyn-
thetic pathway. More complex models
combine descriptions of diffusion of CO2
into the leaves and of the biochemical
processes of photosynthesis.
Plants also respond to elevated CO2 by
reducing stomatal conductance, so most
models also include an effect adjusting leaf
or canopy conductance or transpiration per
se (e.g. Tubiello and Ewert, 2002). In models
that simulate a complete energy balance,
reducing transpiration increases canopy
temperature. Thus, an indirect effect of
elevated CO2 is to warm the plants, which
should further affect photosynthesis,
respiration and development.
Differences among species and cultivars
Qualitatively, the most important physio-
logical processes have proven to be similar
across crop species. Furthermore, soil and
atmosphere processes are largely species
independent. Thus, differences among
species are simulated mainly through
changes in parameters rather than through
 GIS and Crop Simulation Modelling Applications 251
fundamental differences in physiology.
Exceptions include differences between C3
and C4 photosynthetic mechanisms, the
nature of vernalization or photoperiod
responses and how these affect phenology,
and the ability of legumes to fix atmospheric
N. Morphological constraints are also
important, especially with regard to growth
of seeds, storage roots or other economically
important organs. Key parameters that
distinguish among species include response
curves for temperature and CO2, critical and
maximal levels of nutrients, factors for
sensitivity to water or nutrient deficits, and
parameters for potential growth of leaves,
stems, roots and seeds or fruits.
Parameters for differences among culti-
vars can involve phenology, partitioning coef-
ficients and reference organ sizes (e.g.
maximal area of an individual leaf or mass of
a seed). Phenology requires consideration of
the relative duration of different phases, and
responses to vernalization (if present) and
photoperiod. Values of the parameters are
usually determined through iterative param-
eter adjustment and comparison with
observed data from field trials (e.g. Piper et
al., 1996). This calibration process is problem-
atic because it requires that detailed sets of
accurate observations be available. The error
inherent in data from field studies makes it
difficult to discern whether differences
between observed and simulated data are due
to incorrect parameter values or to errors in
the model per se. Various groups are explor-
ing how to use information from genetics or
genomics to parameterize cultivars more reli-
ably (e.g. White and Hoogenboom, 1996; Yin
et al., 2000; Messina et al., 2006).
Crop management
To simulate the growth of a crop, the model
must know how the crop is to be grown,
whether for a real world or hypothetical situ-
ation. Management information includes
the date and manner of planting, the culti-
var used, fertilization and irrigation prac-
tices, and for some crops, harvest practices
(Table 13.2). Tillage and residue manage-
ment may also be considered. The informa-
tion either establishes the initial conditions
for the simulation or modifies aspects of the
environment, such as through addition of N
or water to the soil profile.
Basic application of crop models in
climate change research
Assuming an appropriate model is at hand
and a reference crop production scenario
exists, simulating the effects of climate
change mainly involves running the model
for the weather and CO2 scenarios of inter-
est. For a single site or region, the scenarios
may be specified as fixed (e.g. an increase in
daily mean temperature of 2°C) or relative (a
20% decrease in daily precipitation). These
adjustments may be held constant over the
crop cycle or varied. The choice depends on
the objectives and the source of the climate
change scenario. Because a season might be
unrepresentative of long-term trends, simu-
lations are usually run for 20 or more years.
The requisite weather data may come from
historical records or from weather generator
software that reproduces the statistical
properties of historic conditions (e.g.
Mavromatis and Jones, 1998; Jones and
Thornton, 2003).
A single set of runs can be compared to
equivalent runs using unadjusted weather,
thus providing one estimate of the potential
impact of climate change on economic yield
or a diverse range of other traits. None the
less, such a comparison ignores the poten-
tial that producers will adapt their practices
to the changing environment. We examine
two hypothetical cases, one for soybean and
planting dates and one for maize and N
fertilizer response, to illustrate a few of the
issues that may be relevant. Both studies
assume an increase in CO2 from 380 ppm
(the approximate level in 2005) to 580 ppm.
Soybean planting date
Crop response to planting date is readily
modelled to examine how warming might
affect the potential growing season. For
temperate climates, logical expectations are
that warming would allow earlier or later
252 D. Hodson and J. White

plantings, while elevated CO2 should increase and, as expected, warming reduces the delay
growth and yield. However, warming accel- (Fig. 13.1a). By April, however, longer day
erates development and causes earlier flow- lengths begin to slow development for both
ering and maturity, which would reduce treatments. With an early May planting, the
growth, and at the higher temperatures in warming regime is predicted to slow flower-
summer months, growth might decline ing slightly due to supra-optimal tempera-
further due to a decrease in photosynthesis tures. Note that the model assumes no effect
and increase in respiration. of CO2 on phenology.
For Gainesville, Florida (latitude 29°38´N; The yield responses suggest that the
elevation 10 m), the csm-cropgro-Soybean beneficial effects of elevated CO2 roughly
model predicts that very early plantings result balance the detrimental effects of tempera-
in delayed flowering due to low temperatures, ture up to early May, but subsequently,

(a) 65
Flowering (days after planting)

55

45

35

0
1 Feb 1 Apr 1 Jun 1 Aug 1 Oct
Planting (day of year)
Historical temperature conditions 1.5/3.0°C

(b) 3000
Seed yield (kg/ha)

2000

1000

0
1 Feb 1 Apr 1 Jun 1 Aug 1 Oct
Planting (day of year)
380 ppm/Historical temperatures 380 ppm/1.5/3.0°C
580 ppm/Historical temperatures 580 ppm/1.5/3.0°C

Fig. 13.1.  Simulated response of soybean to planting date (February–September) at Gainesville, Florida.
(a) Flowering response under +1.5°C daily maximum, +3.0°C daily minimum air temperature versus
historical temperature conditions from 1988 to 2001. (b) Seed yield response under +380 ppm CO2 or
+580 ppm CO2 and +1.5°C daily maximum, +3.0°C daily minimum air temperature versus +380 ppm CO2
or +580 ppm CO2 with historical temperatures from 1988 to 2001. Simulations are from csm-cropgro-
Soybean for cultivar ‘Bragg’ with irrigations applied as needed to avoid water deficit.
 GIS and Crop Simulation Modelling Applications 253

elevated CO2 provides a small but consistent (Fig. 13.2b), but not at the other two N levels.
benefit equivalent to 5–10% of the yield Warmer temperatures promote early flower-
expected for historical conditions (Fig. ing (Fig. 13.2c), so a portion of the tempera-
13.1b). For plantings around 1 April, addi- ture effect on yield relates to the shorter
tional yield benefit might be obtained by growth duration (Fig. 13.2d). One interpret-
substituting a later-flowering cultivar. ation of the response to N is that at lower N
levels, yield is limited by N and not assimilate
production. Alternatively, assumptions about
Maize response to warming,
how to model interacting temperature and N
elevated CO2 and N
stresses in the csm-ceres-Maize model may
Maize crop growth was simulated for 25-year merit review.
periods at Palmira, Colombia, an equatorial
location (latitude 3°29´N; elevation 965 m)
with a mean annual temperature of 25°C. A Coupling GIS to crop models
September planting date was used, corres-
ponding to the onset of the rainy season. GIS and simulation models complement each
The crop was assumed to be rainfed, fertil- other for data management, analysis and
ized at 50, 100 or 200 kg N/ha, and other- presentation. Simulation models have
wise well managed. traditionally­ been used on a site-specific
Seed yield declines with increasing basis, but the coupling to GIS is appealing
temperature for the 200 kg/ha N at ambient because it permits the possibility for simul-
(380 ppm) CO2 (Fig. 13.2a) and elevated CO2 taneous investigation of spatial and temporal

(a) (b)
8000 8000
CO2 = 380 ppm CO2 = 580 ppm
Seed yield (kg/ha)

Seed yield (kg/ha)

6000 6000

4000 4000

2000 2000

0 0
0 1 2 3 4 5 6 0 1 2 3 4 5 6
Temperature increase (°C) Temperature increase (°C)
N (kg/ha): 50 100 200 N (kg/ha): 50 100 200
(c) 70 (d) 8000
CO2 = 380 ppm
Flowering (days after planting)

66 6000
Seed yield (kg/ha)

62 4000

58 2000

54 0
0 1 2 3 4 5 6 54 58 62 66 70
Temperature increase (°C) Flowering (days after planting)
N (kg/ha): 50 100 200

Fig. 13.2.  Simulated response of maize to 50, 100 or 200 kg/ha N fertilization at Palmira, Colombia under
temperature increases over historical conditions of +0.5°C to +5.5°C from 1978 to 1997. (a) Seed yield
response under +380 ppm CO2. (b) Seed yield response under 580 ppm CO2. (c) Days to flowering
(response same for all N and CO2 levels). (d) Seed yield response versus days to flowering under +380
ppm CO2. Simulations are from csm-ceres-Maize for cultivar ‘Cargill 111S’ assuming rainfed conditions.
254 D. Hodson and J. White

phenomena. Visualization of model summary examples are given below in order to illustrate
outputs, for example yield response, via a the range of approaches being undertaken.
GIS also adds an extra dimension. As a result,
there has been a rapid growth in the number
Climate change and crop wild relatives
of applications interfacing GIS and simula-
(genetic diversity)
tion models since the late 1980s (Hartkamp
et al., 1999). Multiple examples now exist of
Tools such as FloraMap™ and Homologue™
crop models, typified by the Decision Support
have provided a useful means by which envir-
System for Agrotechnology Transfer (dssat)
onmental niches and priority areas for wild
family, and linked to GIS at a range of spatial
relative diversity can be identified. Incorpor­
scales from field to region (see summary
ation of future climate data into such tools is
table in Hartkamp et al., 1999). Simulations
providing indications on how the environ-
run over large geographical regions extend
ments supporting wild relatives might
the model outputs to areas that have not
change. Using FloraMap™ with HadCM3
been validated, so serve more as a sensitivity
model data, Jones and Beebe (2001) looked
analysis for the model rather than a precise
at predicted wild bean environments in
calculation. However, such assessments do
Central America in 2055. Their conclusion
permit the possibility for the evaluation of
was striking: in five out of the seven countries
multiple scenarios in relative terms within a
studied, the results indicated the virtual
spatial framework. The HarvestChoice
disappearance of suitable wild bean habitat
project (HarvestChoice, 2009a) is taking
by 2055. Jarvis et al. (2001) used a similar
such an approach, attempting to simulate
approach for wild Arachis species (the closest
yield potential of major crops on a continent-
relatives to cultivated groundnut) in South
wide basis under a range of differing techno-
America. Again the predicted scenarios for
logical scenarios (see HarvestChoice, 2009b).
2055 were striking: 12 out of 17 species were
Availability of highly disaggregated data sets,
predicted to go extinct and four of the remain-
both spatial and temporal, is fundamental to
ing five likely to be dangerously threatened. A
this approach, and although progress is being
comparative study of wild relatives of ground-
made, several challenges still remain.
nut (Arachis), potato (Solanum) and cowpea
(Vigna) under future 2055 climate scenarios
reported similar results: high extinction rates,
Case Studies of Applications of GIS decreased range sizes and increased fragmen-
tation of environments (Jarvis et al., 2008).
and Modelling to Climate Change
Such analyses have raised awareness of the
potential threat posed to wild relatives and
The application of GIS-based systems to agro-
the subsequent loss of important genetic
climatic analysis under current climate condi-
diversity. Use of GIS has allowed graphic visu-
tions has already been outlined. The
alization of the decline in suitable environ-
availability of a range of GCM outputs run
ments, highlighting where the major effects
under a suite of emission scenarios is now
might occur and providing a quantitative
permitting similar approaches for potential
assessment of fragmentation patterns.
future climates. With any such approaches it
should always be borne in mind that outputs
from the GCMs are not precise and variation Shifting abiotic and biotic stress
occurs between different models and scenar- distribution
ios. In addition, for agricultural assessments
downscaled GCM results are usually required The previously described mega-environment
and this introduces another set of uncer- concept used by CIMMYT captures
tainty. Despite these caveats, the results of crop-stress related information. Heat stress
such studies can provide useful indications of is an important yield-limiting factor for
the potential magnitude of change and the wheat and this is captured in one of the
spatial variation that may occur. Selected mega-environment­ definitions (ME5).
 GIS and Crop Simulation Modelling Applications 255
Redefin­ition of the mega-environments
based on future climate data derived from
the ccm3 model (Govindasamy et al., 2003),
indicated substantial potential expansion of
these lower potential heat-stressed environ-
ments in South Asia by 2050 (Hodson and
White, 2007 – see Fig. 13.3). Subsequent
incorporation of additional GCM data for
2020 (from HadCM3, CSIRO and CCCMA,
the Canadian Centre for Climate Modelling
and Analysis) also indicated a similar
considerable expansion of heat-stressed
wheat production environments.
Drought stress is another major concern
under climate change. The failed season
model previously described provides a
framework for looking at future scenarios.
Using the HadCM3 A1 scenario for 2050,
Thornton et al. (2006) illustrated the poten-
tial shifts in frequencies of failed seasons
within sub-Saharan Africa. Results obtained
indicated a quite dramatic increase in the
probability of failed seasons across the agri-
cultural regions of Africa. Embedding the
model within a GIS environment permitted
clear visualization of the shifting spatial
distributions.
Changes in the distributions, species
composition and timing of occurrence of
agricultural pests and diseases are other
factors that will undoubtedly respond to
global change, but as a result of complex
dynamics between hosts and pests and large
variation in pest response to climatic condi-
tions and CO2 levels, trends are difficult to
predict. In broad terms, warmer more humid
conditions usually favour insect pests and
diseases. Models such as climex provide
opportunities to determine suitability indi-
ces for particular species under future
climate scenarios (e.g. Sutherst et al., 2000).
Maize in Africa and Latin America
Jones and Thornton (2003) used csm-ceres-
Maize to examine impacts of climate change
on maize production in Africa and Latin
America to 2055. Using GIS, they excluded
non-maize regions and assigned soil data to
each pixel associated with weather data. The
simulations considered four maize cultivars
varying in growth duration, and planting
dates were assigned based on mean onset of
the growing season. Only 50 kg N/ha was
applied so that results would correspond to
low-input, smallholder farming. The results
suggested that climate change would reduce
yields by an average of 10%, but with import-
ant regional variation, especially in moun-
tainous areas.
Rice in Asia
A common concern in climate change stud-
ies is how sensitive projected impacts are to
projections for increased greenhouse gases
and to the GCM used. Masutomi et al. (2009)
compared projections based on differing
Special Report on Emissions Scenarios
(SRES) as used in 14–18 GCMs, using rice
production in Asia as a test case. In the
2020s, all scenarios agreed that the yield-
reducing effects of climate would be large
enough to offset possible benefits from
elevated CO2. Yield variability also increased
with rising CO2. Overall, the results
confirmed that while estimated impacts
varied depending on the SRES and GCM,
trends were consistent in showing that
production will be likely to decrease while
yield uncertainty increases.
Low-cost adaptation strategies for rainfed
and irrigated production in the
Midwestern USA
Easterling et al. (1992) examined adaptation
options with notable detail, considering
planting dates, N levels, and the possibility
of introducing a fallow. Their paper also
stands out because potential adaptations
were selected based on input from experts.
Of 21 potential changes, however, only ten
could be simulated with the epic model.
Earlier planting, longer-season cultivars and
furrow dyking would reduce the impacts of
warming. Beyond adaptations for single crop
species, of course, one can compare how
different crops or crop sequences respond to
climate change (O’Neal et al., 2005; Thomson
et al., 2006).
256 D. Hodson and J. White

(a)

Current
ME1 sites
ME5 sites
Current ME1
Current ME5

(b)

Future (2050)
Future (2050) ME1
Future (2050) ME1

Fig. 13.3.  Comparison of relative distribution of irrigated spring wheat mega-environments (MEs) in
South Asia. ME1 is for favourable climatic conditions, and ME5 is for regions where heat stress is
expected. (a) MEs under current climatic conditions. (b) MEs for a 2050 scenario (2 × CO2, ccm3 model;
Govindasamy et al., 2003). From Hodson and White (2007) reprinted with permission from Cambridge
University Press.
 GIS and Crop Simulation Modelling Applications 257
Yield loss due to rice blast and warming
in Asia
Most simulation studies focus on crop
response to abiotic factors. The study of Luo
et al. (1998) is one of the few cases where a
disease model, for rice blast, was coupled to a
crop model, ceres-Rice, to assess potential
impact of global warming. Tests were run for
30 years of generated weather data from 53
locations in five countries. Yield impacts
varied with region. Blast is favoured by moist
conditions with moderate temperatures, so
impacts were greater in cooler rice producing
regions.
Knowledge, Data, Technology and
Intellectual Constraints
The accuracy of crop models is constrained
by uncertainty over physiological processes
related to climate change. This includes
effects of CO2 and temperature on photo-
synthesis (Crafts-Brandner and Salvucci,
2004) and net crop responses (Long et al.,
2006; Tubiello et al., 2007). There also is
evidence that CO2 affects crop growth and
development through mechanisms besides
carbon fixation and transpiration. Elevated
CO2 can either accelerate or slow develop-
ment, depending on the plant species (Reekie
et al., 1994; Ellis et al., 1995) and affect plant
morphology (Pritchard et al., 1999).
Ignoring whether data for CO2 and
climate change scenarios are accurate (see
Jarvis, Chapter 2, this volume), basic avail-
ability and accuracy of data required for GIS
and modelling still pose major constraints.
Data limitations exist in several key areas.
Soils, crop distributions, land cover and
pest/disease distributions would all be good
examples. Crop distribution data sets are
inaccurate and incomplete even for major
crops at the global to regional scale. The
combination of crop survey and census data
with remote sensing data, to produce grid
cell maps with crops allocated into the most
suitable areas, is a promising approach (Leff
et al., 2004; You and Wood, 2006; You et al.,
2009). However, poor quality inputs often
limit the utility of outputs in certain areas.
These and other data constraints imply that
future change scenarios may often be based
on imperfect current base scenarios. For
simulation models, the list of model inputs
in Table 13.2 indicates the dimensions of the
task. To accurately describe any production
situation, one needs information on manage-
ment. Ideally, the information should be
specified as decision rules, such as for how a
producer decides when to plant rather than
an average planting date.
Standardized formats exist to describe
field experiments (Hunt et al., 2001), and
integrated crop information systems offer
the potential of linking management infor-
mation with crop genetics (e.g. McLaren et
al., 2005). Remote sensing may provide data
for crop distributions, yields and production
cycles (e.g. Lobell et al., 2003) as well as
facilitate high-resolution characterization of
soil and weather conditions (e.g. Minasny et
al., 2008; NASA, 2009).
Development of models and associated
software tools remains a largely individual-
istic process. Hundreds of models have been
programmed, but few have survived past
their initial publication. Modularization of
model components, discussed since at least
1985 (Reynolds and Acock, 1985), should
allow researchers to interchange compo-
nents and focus on science rather than
programming. However, there has been
minimal progress in establishing modelling
frameworks for modules where scientists
can readily test hypotheses about specific
processes. More recently, computer scien-
tists have argued for use of the Unified
Modelling Language (UML) as a way of
separating specific scientific hypotheses
from actual coding of software (Papajorgji,
2005).
Credible studies of crop responses to
climate involve dealing with large sets of
data and potentially millions of simulations,
especially if adaptation is considered. While
the computational challenges are daunting,
the greater challenge is how to devise effi-
cient protocols for selecting the most mean-
ingful scenarios, interpreting the results,
and summarizing outputs for non-
specialists­. GIS-based mapping has special
value for communicating complex data, and
use in climate change might be enhanced
258 D. Hodson and J. White
through animation or dynamic user naviga-
tion interfaces.
Conclusions
GIS and crop simulation modelling will see
increasing use in climate change research
and in applications of research in decision
making. Maps are especially valuable for
allowing people to understand how climate
change impacts, as well as possible adapta-
tions vary, across the landscape.
Examples highlighted in this review illus-
trate how the combination of GIS and crop
models may assist with policy and breeding
decisions in relation to climate change.
Knowledge surrounding the potential shifts
of abiotic and biotic stresses can help guide
prioritization and targeting of key traits
within crop breeding programmes.
Increasingly, options exist to undertake
analysis under a range of future climate
scenarios that incorporate data from a range
of sophisticated GCMs. Such an approach
can lead to probabilistic outputs that can be
used to guide decisions regarding the likely
importance of specific traits in different
geographic regions in the future. In combin­
ation with secondary data sets (e.g. crop
distributions and demographic data) this
can provide useful indicators regarding likely
focus areas for important traits (e.g. drought
and heat stress). Valuable information,
particularly from crop models, may also be
obtained on the potential value of specific
adaptation mechanisms – either in terms of
phenology or crop management.
Similarly, for decisions relating to the
conservation of plant genetic diversity and
plant genetic resources, outputs from a GIS/
modelling-based approach can provide
useful insights. The case studies highlighted
here illustrate how priority regions, either
for in situ conservation of important wild
relatives or for prioritized collection efforts
for ex situ conservation, can be identified. In
both the conservation of plant genetic
resources and the priority setting of breed-
ing traits the lead time to obtain the desired
results (e.g. a new variety or adequate
protection­ of a priority region) can be
considerable. The application of GIS/model-
ling technology within a future climate
framework as outlined in this review is one
way that can guide decision making on an
appropriate time frame.
Limitations of the two technologies per
se relate to our incomplete knowledge of
physiological processes, the availability and
accuracy of data, and implementation of the
tools through software systems. Both tech-
nologies may provide useful insights for
future decision making, but it is unlikely
that they will capture in totality the full
complexity and unpredictability of a rapidly
changing climate.
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14
Statistical Models for Studying
and Understanding Genotype ×
Environment Interaction in an
Era of Climate Change and
Increased Genetic Information

José Crossa, Juan Burgueño and Mateo Vargas

Abstract
Annual crop production will be greatly affected by increases in mean temperature and climate change,
which will be likely to reduce agricultural production and decrease food availability. Plant breeding
will play an important role in developing more sustainable lines and varieties for less favourable
environments that will be subjected to extreme changes in biotic and abiotic stresses. Breeding
cultivars with enhanced tolerance to heat, moisture stress and salinity is essential for long-term
adaptation response to climate change. Multi-environment trials (METs) play a paramount role in
breeding cultivars for general and specific adaptation and yield stability, studying genotype ×
environment (GE) interaction, and predicting the performance of new cultivars in future years and
new locations. METs produce a vast amount of useful data, including not only phenotypic
measurements of cultivars evaluated in different environments but also climatic and soil data as well
as molecular markers representing genetic data. Appropriate statistical models and analyses used to
study response patterns of genotypes and their molecular marker attributes across different
environments undergoing varying climatic changes will be of paramount importance for developing
sustainable and stable cultivars that are resistant/tolerant to diverse biotic and abiotic stresses. In
this chapter, we explain the theoretical basis of several statistical models and their application for
explaining the climatic and genetic causes of GE interaction.

Introduction climatic fluctuations from year to year. In

The urgent need to increase grain produc-
tion presents a serious challenge to agricul-
tural systems globally and locally; the
increase must come from raising grain yield
per unit area, given that the degree to which
the area of cultivated land can be expanded
is very limited. The Green Revolution
enhanced overall agricultural productivity in
many areas of the world by generating
improved wheat varieties with high yield
potential under optimal high-input environ-
ments. However, low-input and less favour-
able environments have poor agroclimatic
potential and are highly affected by biotic
and abiotic stresses that show marked
© CAB International 2010. Climate Change and Crop Production (ed. M.P. Reynolds) 263
these less favourable environments, the
plant breeding approach should be different
from those used in more favourable high-
input environments. Furthermore, in the
near future many favourable environments
may become less favourable (in terms of soil
fertility and general climatic conditions) and
be plagued by biotic and abiotic stresses due
to extreme climate change. Climate change
is due to many factors such as rising global
mean temperatures, increased intensity and
frequency of storms, drought and flooding,
weather extremes, and altered hydrological
cycles and precipitation patterns. Annual
crop production will be greatly affected by
increases in mean temperature throughout
264 J. Crossa et al.
this century, and climate change will be
likely to reduce agricultural production and
decrease food availability (Lobell et al.,
2005).
Plant breeding will play a paramount role
in developing more sustainable farming
systems in less favourable environments
subject to extreme biotic and abiotic stresses
(see Chapters 4–8, this volume). Developing
cultivars with enhanced tolerance to heat
and moisture stress and salinity is essential
to a long-term adaptation response to
climate change. In developing crops for the
21st century, breeders must keep in mind
that production environments will be more
variable and more stressful, yearly climate
variation will be greater, and field sites and
test environments will essentially be rapidly
moving targets. Appropriate breeding strat-
egies will ensure the development: (i) in the
long term, of improved varieties, lines and
hybrids with adaptation to less favourable
environments and high yield stability; and
(ii) in the short term, of appropriate varieties­,
lines and hybrids to meet local farmers’
needs. Breeding strategies are based mainly
on breeders’ in-depth knowledge of their
germplasm in general and of how genotypes
will respond under different environmental
conditions.
Regardless of the breeding strategy used,
in any breeding programme multi-
environment­ trials (METs) are essential for
assessing varietal adaptation and stability,
and for studying and understanding geno-
type × environment (GE) interaction. For
example, significant progress has been made
in maize grain yield under drought stress by
selecting for component traits such as kernel
set, rapid silking and reduced barrenness in
METs. GE interaction refers to the differen-
tial response of a set of plant materials (such
as lines, open-pollinated varieties or popula-
tions, etc., referred to as ‘genotypes’) when
evaluated in a set of environments charac-
terized by certain soil, climatic, pest, disease
and management conditions (referred to as
‘environments’) in a given location and year.
In general, GE may be due to heterogeneity
of within-environment variance (HV) or
scale changes, or to crossover interaction
(COI) or changes in rank of genotypes in
different environments. In agricultural
production, the most important GE is that
due to COI.
Conventional breeding in conjunction
with marker assisted selection (MAS) may
bring about significant and predictable
incremental improvements in the drought
tolerance of new maize lines and hybrids
(Bänziger and Araus, 2007). Likewise, the
genetic dissection of maize performance in
drought-prone environments has greatly
benefited from the use of DNA markers
(Ribaut and Ragot, 2007). The use of MAS in
plant breeding has increased consistently
since 1980, and molecular markers are now
considered a valuable breeding tool.
Advances in high-throughput genotyping
have reduced the cost of using molecular
markers, and their abundance and low cost
have led to selection based only on molecu-
lar markers (called marker-assisted recur-
rent selection, or MARS). Applying MARS
for one cycle based on phenotypic and
marker scores followed by two or three cycles
of selection based solely on marker score
information has increased genetic gains.
Genome-wide dense marker maps are now
available for many plant and animal species,
and genome-wide selection has become an
interesting option for increasing genetic
gains in different crops and animals
(Bernardo and Yu, 2007).
Important challenges are how: (i) marker
information should be incorporated into
statistical models that could be useful for
predicting genetic values in animal and plant
breeding programmes, or for predicting
diseases; (ii) the large number of candidate
genes known to have specific trait effects
could be used in a practical breeding
programme; (iii) the large number of envir­
onmental variables and pests affecting
genotypes­ in METs could be used to better
predict genotypic and phenotypic perform-
ance so that the best genotypes are selected
as parents for the next generation; and (iv)
the powerful computer algorithms used in
crop modelling and simulation methods
could help breeders to better achieve their
goals.
The massive accumulation of genetic and
environmental data confirms the urgent
 Statistical Models for GE Interaction 265
need for suitable and efficient bioinforma­
tics, biometrical and statistical methods to
assess and incorporate GE studies into
conventional as well as MARS and genome­
wide selection breeding schemes for less
favourable environments. The objective of
this chapter is to describe the theory and
practical applications of statistical models
and methods normally used for studying
and understanding GE and how they can be
applied in combination with molecular
markers in plant breeding.
Phenotypic Values, Genotypic Values and
Environments
Before describing statistical models for
studying the response of genotypes under
different environmental conditions, we
should explain that phenotypic (observed)
values are a function of genes that produce
genotypic (unobserved) values under certain
environmental conditions. This is clearly
explained by Bernardo (2002) for modelling
the phenotypic value of the kth individual
having a genotype AlAm (locus A has two
alleles­, lth and mth), which is in turn affected
by a non-genetic component elmk . Then, the
phenotypic value will be Plmk = genetic
+ non-genetic = Glm + elmk or Plmk = µ + g lm
+ elmk (for the deviation from the popula-
tion mean, µ , of g lm = Glm − µ ) assuming
the genotypic value g lm and the non-genetic
elmk values are uncorrelated. In general,
genotypic values include additive, and domi-
nance within locus and all types of epistatic
effects between loci. The expected value of
Plmk for all individuals with genotype AlAm is
equal to the genotypic value g lm plus the
expectation of the non-genetic effects elmk .
Under the assumption that the expectation
of elmk is equal to zero, then the expected
value of Plmk = µ + g lm and the expected value
of Plmk across all genotypes (and not only
genotype AlAm) is µ (implying that the
expected value of g lm is, in fact, zero). This
two-allele locus model can be extended to
any number of loci.
Although genotypic values cannot be
measured directly, they are estimated based
on phenotypic values and environmental
effects. This is the main reason why breeding
programmes need to have not only a clear
set of genotypes to be tested but also a clear
set of target environments where those
genotypes should be tested. Therefore, in
METs, just as genotypic values (estimated
based on phenotypic values) depend on the
environments in which the genotypes are
grown and the trait measured, so environ-
mental values depend on the genotypes
grown in those environments. In most
METs, the genotypic values g lm for different
genotypes are different in different environ-
ments; this constitutes GE.
The Basic Two-way Fixed-effect Linear
Model
Early approaches to GE analyses included
the conventional fixed-effect two-way model
with sum to zero constraints running over
indices. The empirical response y ijr of the ith
genotype (i = 1, 2, …, I) in the jth environ-
ment (j = 1, 2, …, J) with r replications in
each of the I × J cells is expressed as:
y ijr = µ + τi + δ j + ( τ δ )ij + eijr (14.1)
where µ is the grand mean (over all geno-
types and environments), τi is the additive
effect of the ith genotype, δ j is the additive
effect of the jth environment, ( τ δ )ij is the
non-additivity interaction (GE) of the ith
genotype in the jth environment (forming
matrix Z), and eijr is the within-environment­
error associated with the ith genotype in the
jth environment and the rth replicate.
The phenotypic value averaged across
replicates in each environment is y ij , and
the least squares estimates of the genotypic
effect and the environmental effects are
τˆ i = y i .. − y ... (which satisfies the constraint
∑ τˆ i = 0 ) and δˆ j = y.j. − y... (which satisfies
i
the constraint ∑ δˆ
j
j = 0 ) (Table 14.1), where
y ... is the least squares estimate of the overall
mean µ and y i.. is the mean of the ith geno-
type averaged across environments and
replicates­, and y .j. is the mean of the jth
environment across all genotypes and
replicates­. Therefore, the least squares
266 J. Crossa et al.

estimate­ of the GE term in Eqn 14.1 is decomposition (SVD) after adjusting for the
( τˆ δˆ )ij = z ij = y ij. − y i.. − y .j. + y ... (which satis- additive (linear) terms. The first two compo-
fies the constraints ∑∑ ( τδ
ˆ ˆ )ij = nents can be displayed in a graph called a
i j biplot. Zobel et al. (1988) and Gauch et al.
∑ ( τδ
j
ˆ ˆ ) = ∑ ( τδ
ij
ˆˆ)
i
ij = 0 ) (Table 14.2). (2008) named Eqn 14.2 the Additive Main
Effects and Multiplicative Interaction
Note that the notation in Eqn 14.1 can be (AMMI) model. Other types of linear–
used for models with fixed, mixed, or random bilinear­models, described by Cornelius et al.
effects. For a complete random model, it is (1996), are:
assumed that τi , δ j and ( τδ)ij are normally
and independently distributed, with vari- the Sites (environments) Regression (SREG)
ances σ2τ , σ2δ and σ2τδ , respectively. model:
t
y ij = µ j + ∑ λ k α ik γ jk + εij (14.3)
Fixed-effect Linear–Bilinear Models k =1
the Genotypes Regression (GREG) model:
Williams (1952) was the first to link the Eqn t

14.1 model with principal components (PC) y ij = µ i + ∑ λ k α ik γ jk + εij (14.4)

k =1
analysis by considering the model the Completely Multiplicative Model
y ij = µ + τi + λα i γ j + εij where λ is the larg- (COMM):
est singular value of ZZ′ and Z′Z (for Z = t
y ij − y i. ), and α i and γ j are the correspond- y ij = ∑ λ k α ik γ jk + εij (14.5)
ing eigenvectors. Gollob (1968) and Mandel k =1
(1969, 1971) rediscovered and extended and the Shifted Multiplicative Model
Williams’ (1952) work by consideringt
the (SHMM):
bilinear GE term as ( τ δ)ij = ∑ λ k α ik γ jk . Thus, t
k =1 y ij = β + ∑ λ k α ik γ jk + εij (14.6)
the general formulation of the linear– k =1
bilinear model is: The SHMM was the first linear–bilinear
t model that, along with other statistical tools,
y ij = µ + τi + δ j + ∑ λ α γ jk + εij (14.2) was used for identifying subsets of geno-
k ik
k=1 types or environments in which genotypic
where the constant λ k is the singular value rank changes would be negligible (Cornelius
of the kth multiplicative component that is et al., 1992, 1993; Crossa and Cornelius,
ordered λ 1 ≥ λ 2 ≥ ... ≥ λ t ; the α ik elements 1993; Crossa et al., 1993, 1995). The SREG
are elements of the kth left singular vector (Crossa and Cornelius, 1997) model is very
of the true interaction and represent geno- useful in plant breeding because the bilinear
typic sensitivity to hypothetical environmental terms contain both the main effects of geno-
factors represented by the kth right singular types (G) and GE. The SREG model has been
vector with elements γ jk . The α ik and γ jk preferred to SHMM for grouping environ-
elements satisfy the ortho-normalization ments without genotypic rank change
constraints ∑ α ik α ik′ = ∑ γ jk γ jk′ = 0 for k ≠ k′ (Crossa and Cornelius, 1997). The interac-
tion parameters α ik and γ jk in the bilinear
∑α ∑γ
i j
and 2
= 2
= 1. When Eqn 14.2 is
i
ik
j
jk
terms model the behaviour of genotypes and
saturated, the number of bilinear terms is t environments, and when ( α i 1 , α i 2 ) and
= min(I – 1, J – 1), and for any smaller value, ( γ j 1 , γ j 2 ) are plotted together in the biplot
the model is said to be truncated. The GE (Gabriel, 1978), useful interpretations of
interaction parameters λ k , α ik and γ jk are the relationships between genotypes, envir-
estimated from the data. onments, and GE are obtained. In the biplot,
Gabriel (1978) described the least squares the interaction between the ith genotype
fit of Eqn 14.2 and explained how the resid- and the jth environment is obtained by
ual matrix of the GE term, Z = y ij − y i. − projecting one vector on to the other. In the
y .j + y .. , is subjected to singular value AMMI model, the composition of the two-

Table 14.1.  Least squares estimates of genotypic and environmental effects for a two-way table of genotypes and environments with i = 1, 2, …, I genotypes,
j = 1, 2, …, J environments and r replicates.
Marginal mean
Environment 1 Environment 2 . . Environment J of genotypes Estimate of genotypic effect (τi )

Statistical Models for GE Interaction

Genotype 1 y11. y12.  .  . y1J . y1.. τ̂1 = y1.. − y...

Genotype 2 y 21. y 22.  .  . y 2J . y 2.. τ̂2 = y 2.. − y...

.   .   . . .   .   .     .
.   .   . . .   .   .     .
Genotype I yI 1. yI 2. . . yIJ . yI.. τ̂I = yI.. − y...

Marginal mean of y.1. y.2.  .  . y.J . µˆ = y...    –

environments

Estimate of δˆ 1 = y.1. − y... δˆ 2 = y.2. − y...  .  . δˆ J = y.J . − y...   –    –

  environmental
   effect (δ j )

267
268 J. Crossa et al.

Table 14.2.  Least squares estimate of the genotype × environment (GE) term in Eqn 14.1 is
(τδ)ij = zij = yij . − yi .. − y. j . + y with i = 1, 2, …, I genotypes, j = 1, 2, …, J environments and r replicates.
Environment 1 Environment 2 . . Environment J
 
Genotype 1 y11. − y1.. − y.1. + y... y12. − y1.. − y.2. + y...   . . y1J . − y1.. − y.J . + y...
   
Genotype 2 y 21. − y 2.. − y.1. + y... y 22. − y 2.. − y.2. + y... . . y 2J . − y 2.. − y.J . + y...
   
. . . . . .
 
. . .   . . .

Genotype I yI 1. − yI .. − y.1. + y... yI 2. − yI .. − y.2. + y... yIJ . − yI .. − y.J . + y...

way I × J matrix to be subjected to singular  Can biplot analysis contribute to detect-

value decomposition is shown in Table 14.2,
where only the GE interaction (see Eqn 14.2)
is modelled by the bilinear terms. In the
SREG model, the bilinear term models the
main effects of genotypes (G) plus GE inter-
action (usually called a GGE biplot), and the
composition of the two-way I × J matrix to
be subjected to singular value decompos­
ition (see Eqn 14.3) is shown in Table 14.3.
Recently there was an ongoing debate
examining the merits and demerits of AMMI
versus GGE biplots for genotype and envir-
onment identification (Yan et al., 2007;
Gauch et al., 2008). In a recent article, Yang
et al. (2009) pointed out the advantages and
disadvantages of these fixed effects linear–
bilinear models and discussed relevant issues
concerning the use of biplot analysis as a
descriptive statistical tool. The authors
pointed out that several issues affect the
validity of such analysis but are generally
ignored by the current biplot literature.
Some of these issues are:
 What if genotypes or environments, or
both, are random effects?
ing crossover interaction?
 How relevant is biplot analysis for under-
standing the nature and causes of inter-
action?
Mixed-effect Linear–Bilinear Models
What if genotypes or environments, or
both, are random effects?
A mixed-model analogue of biplot analysis
has been developed using the factor analytic
(FA) model for approximating the variance-
covariance GE structure (Piepho, 1998;
Smith et al., 2002). Research conducted by
Crossa et al. (2006) and Burgueño et al.
(2008) described how to model variance-
covariance GE and GGE using the FA model
and how to incorporate the additive (rela-
tionship A) matrix and the additive × addi-
tive covariance matrix into the FA model
based on pedigree information. Burgueño et
al. (2008) also described the equivalence
between SREG2 and FA(2) for finding

Table 14.3.  Least squares estimates of the combined effects of genotype (G) plus the genotype ×
environment (GE)  τi + (τδ)ij  = zij = yij . − y. j . with i = 1, 2, …, I genotypes, j = 1, 2, …, J environments and
r replicates.
Environment 1 Environment 2 . . Environment J

Genotype 1 y11. − y.1. y12. − y.2. . . y1J . − y.J .

Genotype 2 y 21. − y.1. y 22. − y.2. . . y 2J . − y.J .

. . . . . .
. . . . . .

Genotype I yI 1. − y.1. yI 2. − y.2. yIJ . − y.J .

 Statistical Models for GE Interaction 269
subsets of genotypes and environments
without COI.
Factor analytic and sites regression
models for assessing crossover genotype
× environment interaction
In the FA model, the random effect of the ith
genotype in the jth environment ( g ij ) is
expressed as a linear function of latent
variables x ik with coefficients δ jk for k = 1,
2, … t,t plus a residual, ηij , i.e.
g ij = µ j + ∑ x δ jk + ηij , so that the ijth
k =1 ik
cell mean can be written as y ij = g ij + ε ij .
With only the first two latent factors being
retained, g ij is approximated by
g ij ≈ µ j + x i 1 δ j 1 + x i 2 δ j 2 + ηij . Therefore,
SREG2 (Eqn 14.3) can be perceived as
consisting of a set of multiple regression
equations (one for each environment), each
regression equation consisting of an envir-
onmental mean or environmental effect as
intercept plus two terms for regression on
two genotypic regressor variables, α i 1 and
α i 2 (either observed or latent), with γ j 1
and γ j 2 as the regression coefficients. Thus
there is a clear connection between the
SREG2 and the FA(2) models, as described
by Burgueño et al. (2008). A similar connec-
tion between the AMMI2 and FA(2) models
was also established by Smith et al. (2002).
Under principal component rotation, the
directions and projections of the vectors of
FA(2) and SREG2 in the biplot are the same.
Therefore, the property of SREG by which
the first principal component of SREG2
accounts for non-crossover interaction (non-
COI) and the second principal component of
SREG2 is due to COI variability should hold
for FA(2) as well. However, the absolute
values of genotypic and environmental
scores under the FA(2) and SREG2 models
may not necessarily be the same because
shrinkage is involved in Best Linear Unbiased
Predictions (BLUPs) (Henderson, 1984) of
random effects in the FA(2) model but not in
least squares estimates of fixed effects in the
SREG2 model. Other important differences
between SREG and FA are: (i) the standard
errors of the estimable functions of fixed
effects under SREG differ from those of
predictable functions of a mixture of fixed
and random effects under FA; and (ii) FA
models are more flexible in handling unbal-
anced data (the SREG model does not handle
missing data).
Detecting Crossover Interaction
Under Fixed and Mixed Effects
Linear–Bilinear Models
Can biplot analysis help detect crossover
interaction?
The most important GE in agriculture is COI
(Cornelius et al., 1993). In the absence of
COI, GE is simply due to differences in scales,
and the best genotype in one environment
remains the best in all other environments.
The usual AMMI2 biplot analysis does not
distinguish COIs from non-COIs. A SREG1
biplot based on a constrained singular value
decomposition (SVD) non-COI PC1 solution
(Crossa and Cornelius, 1997) has been used
to predict the absence of COIs based on
earlier work on a rank-one shifted multiplic­
ative model (SHMM1) by Cornelius et al.
(1992). If the SHMM1 model is an adequate
approximation to two-way GE data and the
primary effects of environments (PC1 scores)
are either all non-positive or non-negative,
then the SHMM1 model has the two propor-
tionality properties. First, differences
between genotypes in any single environ-
ment are proportional to genotypic differ-
ences in any other environment. Secondly,
differences between environments in terms
of the performance of any single genotype
are proportional to those of the performance
of any other genotype. The second propor-
tionality restriction is not required for assess-
ing genotypic non-COI status and is removed
in the SREG1 model. If the PC1 scores have
different signs, SHMM1 and SREG1 biplots
show the presence of COIs. The SHMM2 and
SREG2 biplots of the first two PCs would
represent the graph of non-COI variation
(PC1) versus COI variation (PC2).
Detection of COI using SREG (and
SHMM) has generally been done within the
270 J. Crossa et al.
fixed effect linear–bilinear framework. The
approach proposed by Crossa et al. (2004)
uses the fixed linear–bilinear SREG and
SHMM models for constructing the cluster-
ing of environments and genotypes with
non-COI, and subsequently uses a linear
mixed model to test the statistical hypothe-
sis of perfect genetic correlations between
environments or genotypes within the
subset. Yang (2007) recognized that in
statistical analyses of METs, either geno-
types or environments, or both, should be
considered as random effects and, therefore,
COI detection must consider that the differ-
ence between genotypic effects in a random
environment is a predictable function that
involves Best Linear Unbiased Estimators
(BLUEs) as well as BLUPs.
Burgueño et al. (2008) proposed an inte-
grated methodology for: (i) clustering envir-
onments and genotypes with negligible COI
based on results obtained from fitting FA to
MET data; and (ii) detecting COI using
predictable functions based on the linear
mixed model with FA and BLUPs of geno-
types. The authors were able to discriminate
COI from heterogeneity of variances (HV).
The advantages of this methodology are
Fig. 14.1.  Biplot from the factor analytic (FA(2)) model of maize grain yield data including nine genotypes
(A, B, C, D, E, F, G, H, I) and 20 environments (1–20) (adapted from Burgueño et al., 2008).
that: (i) it allows researchers to use a more
realistic statistical model with fixed as well
as random effects; (ii) the association among
environments is taken into account and
modelled; (iii) the association among geno-
types is easily introduced (although it is not
included in Burgueño et al., 2008); and (iv)
the approach can be used with unbalanced
and missing data.
Burgueño et al. (2008) used the linear–
bilinear mixed model methodology based on
FA(2). They demonstrated the use of this
approach in two data sets. One data set
consists of grain yield from an International
Maize and Wheat Improvement Center
(CIMMYT) maize MET with nine genotypes
(A, B, C, D, E, F, G, H, I) arranged in a rand-
omized complete four block design evalu-
ated in 20 international environments. The
biplot in Fig. 14.1 gives general descriptive
patterns of genotypes and environments,
and makes it possible to identify extreme
pairs of genotypes and sites with COI, for
example, genotypes D and H with environ-
ments 11 and 8. However, the biplot by itself
does not clearly delineate the subsets of
environments and genotypes with statistic­
ally significant COI. After clustering
 Statistical Models for GE Interaction 271

environments­ and genotypes based on the
mixed linear–bilinear model, the final
subsets of environments with negligible COI
are subsets (1-3-10), (2-6-7-19-14), (4-5-16-
9-17-20-15), (11-13-12-18), and the single-
member subset (8), whereas the final subsets
of genotypes with negligible COI are
(A-B-C-G) and (D-E-F-I), with H as a single-
member group.
Results indicate that when one environ-
mental subset or one genotypic subset was
considered, no significant COI was found.
When subsets of environments located in
opposite quadrants of the biplot in Fig. 14.1
are combined, there is a greater increase in
the number of significant COIs than when
subsets of environments from the same
quadrant of the biplot are combined (Table
14.4). From a breeder’s perspective, it may
be important to consider combining certain
environmental subsets into one larger
cluster­ that may better represent certain
hypothetical target populations of environ-
ments. When environment (8) is combined
with (1-3-10) (both subsets with negative
loadings), no significant COIs are added, but
when (8) is combined with (4-5-9-15-16-17-
20), the number of significant COIs increases
to 12 (Table 14.4). Environment 8 is differ-
ent from all other environmental subsets
except subset (1-3-10). These results are in
agreement with a plant breeder’s main inter-
est, which is developing genotypes with local
as well as wide adaptation. This can be better
achieved by stratifying environments (and/
or genotypes), which in turn increases selec-
tion gains at both regional and local levels.
Regions and subregions may be better delin-
eated based on COI and non-COI. This
approach should be useful for finding poten-
tial new subsets of regions and subregions
that could be affected by new climate change,
drought and/or heat stress. Since climate
change is very dynamic and can be drastic
year after year, data from successive METs
in several years should be systemat­ically
analysed to find response patterns of geno-
types to new environmental conditions.

Table 14.4.  Total number of tetrads among subsets of environments and genotypes, total number of
significant tetrads, number (n) and percentage (%) of significant COI, and number (n) and percentage
(%) of significant non-COI due to heterogeneity of variance (HV) (adapted from Burgueño et al., 2008).
Significant Significant Significant non-COI
tetrads COI due to HV
Subsets Total tetradsa n % n % n %
---------------------------------------------------------- Among subsets of environments ---------------------------------
(1-3-10)(4-5-9-15-16-17-20) 756 135 17.86 19   14 116   86
(1-3-10)(11-12-13-18) 432 54 12.50 21   39 33   61
(1-3-10)(2-6-7-14-19) 540 25 4.63 11   44 14   56
(1-3-10)(8) 108 2 1.85 0    0.0 2 100
(4-5-9-15-16-17-20)(11-12-13-18) 1008 51 5.06 0    0.0 51 100
(4-5-9-15-16-17-20)(2-6-7-14-19) 1260 39 3.10 0    0.0 39 100
(4-5-9-15-16-17-20)(8) 252 61 24.21 12   20 49   80
(11-12-13-18)(2-6-7-14-19) 720 58 8.06 0    0.0 58 100
(11-12-13-18)(8) 144 39 27.08 4   10 35   90
(2-6-7-14-19)(8) 180 22 12.22 3   14 19   86
Total 6840 567 8.29 70 12.3 497   87.7
-----------------------------------------------------------Among subsets of genotypes--------------------------------------
(A-B-C-G)(D-E-F-I) 3040 315 10.4 26 8.3 289   91.7
(A-B-C-G)(H) 760 40   5.3 6 15.0 34   85.0
(D-E-F-I)(H) 760 212 27.9 38 17.9 174   82.1
Total 6840 567   8.29 70 12.3 497   87.7
a Number of tetrads counted is within subsets of environments and genotypes when one environmental subset and one

genotypic subset are considered and between subsets of environments and genotypes when two subsets of
environments or genotypes are considered.
272 J. Crossa et al.
Incorporating External Covariables
for Explaining Genotype ×
Environment Interaction
This section is related to the issue outlined
by Yang et al. (2009), which is how relevant
is biplot analysis for understanding the
nature and causes of interaction? Factorial
regression (FR) or partial least squares (PLS)
analysis (e.g. Vargas et al., 1999; van Eeuwijk
et al., 2005) is useful for studying the effects
of both genetic and environmental covari­
ables and to develop functional relationships
and predictability with explanatory covari­
ables. The structural equation model (SEM)
using endogenous and exogenous variables
is a useful alternative for overcoming some
of the limitations of the FR and PLS
approaches.
Linear models for mapping quantitative
trait loci (QTLs) and adding external
covariables for studying QTL ×
environment interaction (QEI) analysis in
genetics and plant breeding
In important maize growing areas of the
world, grain yield reduction is caused by
drought at flowering time as well as low
nitrogen content in the soil. Drought delays
silking, increases the anthesis–silking inter-
val (ASI) and, therefore, decreases grain
yield. Thus, under drought stress, selection
for short ASI in maize should be correlated
with grain yield improvement, and ASI
becomes an important secondary trait with
relatively high heritability and more stabil-
ity than grain yield. Nevertheless, few stud-
ies have been conducted on mapping QTLs
responsible for the expression of morpho-
logical traits under abiotic stresses.
In plant breeding, much research is
directed at locating regions of the chromo-
somes that are involved in the physiological
processes underlying phenotypical traits.
These regions are called QTLs. When these
regions differ between genotypes in relation
to changes in the environment, QTL × envir-
onment interaction (QEI) occurs. The statis-
tical problem can be interpreted as a
multivariate multiple regression of pheno-
typic traits as observed over a set of environ-
ments on a set of genetic predictors. FR
provides a suitable framework for QEI analy-
sis. Crossa et al. (1999) give examples of how
FR can be used for assessing the chromo-
somal location of QTLs and QEI and the
importance of their effects.
There are approaches in which the GE is
modelled directly using regression on envir-
onmental (and/or genotypic) variables, rather
than regression on the environmental mean.
A useful linear model for incorporating exter-
nal environmental (or genotypic) variables is
the FR model (Denis, 1988; van Eeuwijk et al.,
1996). FR models are ordinary linear models
that approximate the GE effects of Eqn 14.1
by the products of one or more of the follow-
ing: (i) genotypic covariables (observed) ×
environmental potentialities (estimated); (ii)
genotypic sensitivities (estimated) × environ-
mental covariables (observed); and (iii) scale
factor (estimated) × genotypic covariables
(observed) × environmental covariables
(observed). The aim of FR is to replace, in the
GE subspace, genotypic and environmental
factors with a small number of genotypic and
environmental covariables. Vargas et al.
(2006) further developed the statistical
approaches described by Crossa et al. (1999)
and van Eeuwijk et al. (2000, 2002) for model-
ling QTLs and QEI. The main objectives of
their research were to demonstrate the use
of: (i) FR for estimating effects and locations
of QTLs and QEI; and (ii) FR for modelling
and interpreting QEI in terms of products of
genetic predictors and environmental vari­
ables.
In FR, genotypic covariables, xa (a = 1 …
A) with values xia, can be introduced for the
genotypic main effect, Gi:
Gi = x ia ρa + residual, where ρa is the regres-
sion coefficient for the regression of Gi on xa.
For more than one genotypic covariable, this
A
becomes Gi = ∑ x ia ρa + residual. When the
a=1
genotypic covariable xa is replaced by genetic
predictors xq (when attempting to map
QTLs), the FR framework can also be used to
do a genome scan for QTL effects. Analogous
to the genotypic main effect, in FR, the envir-
onmental main effect, Ej, can also be regressed
on environmental covariables, zb with
 Statistical Models for GE Interaction 273
values zjb. The corresponding partitioning is
E j = z jb βb + residual for one environmental
B
covariable, or E j = ∑ z jb βb + residual for
b=1
multiple environmental covariables. The
parameters βb represent the regression
coefficients of the regression of the environ-
mental main effect on zb.
Within a QTL analysis by FR, a multiple
QEI model follows easily from models for
Q
GE: (GE)ij = ∑ x iq ρ jq + residual, where ρjq
q=1
represents a QEI effect, i.e. a differential QTL
expression in relation to the main effect QTL
expression, for the qth QTL in environment j.
QEI for a QTL q′ can be further modelled by
regressing it on an environmental covariable,
zb: (GE)ij = ν q ' b x iq ' z jb + residual. For multiple
QTLs, this generalizes to:
Q B
(GE)ij = ∑ ∑ ν qb x iq z jb + residual.
q=1 b=1
One or more QTL main effects can be
tested by comparing the model
Q
y ij = µ + ∑ x iq ρq + E j + residual with the
q=1
model y ij = µ + E j . When main effect QTL
expression and QEI are considered
together, this is equivalent to fitting
different QTLs to each environment. A
specific test for QEI compares
Q Q
y ij = µ + ∑ x iq ρq + E j + ∑ x iq ρ jq + residual to
q=1 q=1
Q deviations from the regression (F =
y ij = µ + ∑ x iq ρq + E j + residual. F-tests can
q=1
be constructed from ratios of regression
mean squares to the independent error
term.
Table 14.5 shows parts of the analysis of
variance table for one example comprising a
population of F2-derived F3 families evalu-
ated across eight environments differing in
the level of drought stress and soil nitrogen
content, at position 140 cM of chromosome
1 (Vargas et al., 2006). The first part shows
the usual analysis of variance for a two-way
table of grain yield measured in 211 geno-
types with partitioning of the joint effect of
G+GE into G and GE effects. The middle part
shows the variability due to QTL+QEI effects
in parts of the genome other than chromo-
some 1 (i.e. due to QTLs on chromosomes
2–10), the variability due to G+GE after
correction for QTLs on the other chromo-
somes, and the corresponding partitioning
into G and GE components. Approximately
28.8% of the original G+GE was associated
with QTLs on other chromosomes. The last
part shows the partitioning of G+GE
adjusted for the QTLs on chromomosomes
2–10 into variation due to QTL+QEI at
pos­ition 140 cM of chromosome 1 and
deviations­from the QTL-model.
For grain yield, Fig. 14.2 depicts the
profile of R2QTL, R2QEI and R2QTL+QEI and the
corresponding critical values for α = 0.01
based on 1000 randomizations. There is
good reason to believe that there are envir­
onment-specific QTLs between 105 cM and
180 cM of chromosome 1 (Fig. 14.2)
(QTL+QEI and QEI effects were both signifi-
cant). In contrast, only main effect QTLs
were observed in other chromosomes. The
QEI at the end of chromosome 4 and near
the end of chromosome 9 were ignored
because those QEI peaks did not coincide
with the corresponding QTL+QEI peaks. A
significant dominant main effect QTL was
also found on chromosome 4 (not shown).
The environmental covariable that
explained the QEI best, at 77.6%, was mini-
mum temperature during flowering (Table
14.5). The effect of this environmental
covariable was highly significant by an F-test
for the regression mean square over the
76.675/3.686 = 20.8, p = 0.0038), and even
more so when the denominator in the F-test
was the intra-block error.
Linear mixed models for multitrait multi-
environment QTL analysis
A general formulation of a linear mixed
model for the multitrait multi-environment
(MTME) is presented by Malosetti et al.
(2008). The initial model is y = Xβ + Zu + e.
The response vector y is modelled by a set of
fixed effects collected in vector βb and random
effects collected in vectors u and e; X and Z
are design matrices assigning fixed and
random effects to the observations. Random
genetic effects are assumed to be normally
distributed, u ~ N(0, G), with G the genetic
274 J. Crossa et al.

Table 14.5.  Partitioning of yield variation at position 140 cM of chromosome 1. For comparison, an error
estimated from the median intra-block error was 0.75 (adapted from Vargas et al., 2006).
Source of variation Degrees of freedoma Sum of squares Mean squares
Environment (E)     7 12777.169 1825.310
G + GE 1680   3212.868     1.914
   QTL + QEI chrom.b 2–10          –          925.806      –
   G + GE chrom. 1 adj.b       1680         2287.062      –
     F2 family (G) adj.           210            693.358     3.302
     GE adj.          1470           1593.704     1.084
G + GE chrom. 1 adj. 1680         2287.062      –
   QTL + QEI chrom. 1 140 cM       8 153.775    19.222
     QTL main effect        1     54.986    54.986
     QEI        7     98.789    14.113
       Min. temp. flow.b         1         76.675    76.675
       Residual QEI         6         22.114     3.686
Deviations 1672 2133.287     1.276
a For the correction of the grain yield data due to genetic effects on chromosomes 2–10, degrees of freedom might be

discounted.
b chrom., chromosome; adj., adjusted; Min. temp. flow., minimum temperature during flowering.

8
QTL+QEI
7

6
QEI
5
R2 additive

4
QTL
QTL+QEI
3
QTL
2
QEI
1

0
0 20 40 60 80 100 120 140 160 180 200 220 240 260
Position (cM)

Fig. 14.2.  Profile of R2 for the additive effects of QTL (____), QEI (..…), and QTL+QEI (_--_) on grain yield
for chromosome 1 (additive). The horizontal lines mark the appropriate threshold for the effects QTL+QEI,
QTL, and QEI (adapted from Vargas et al., 2006).

(co)variance matrix (vcovG). Finally, e is a effect of a putative QTL as follows:

vector of non-genetic residuals associated
with each observation and normally distrib-
uted, e ~ N(0, R). The phenotypic (co)vari-
ance is given by V(y) = ZGZ′ + R. From a
breeder’s point of view, the vcovG is of special
interest as it reflects the magnitude and
pattern of relationships between genetic
effects. A QTL model arises by including the
y = Xβ + X QTL + Zu * +e. The extra term in
the model is composed of a design matrix
XQTL, which is derived from molecular
marker information and a vector of fixed
QTL effects (αα). In an MTME model, vector
α has dimensions JK × 1 and contains the
additive genetic QTL effects for all the traits
in each of the environments. The random
 Statistical Models for GE Interaction 275
genetic effects, now collected in a vector u*,
result from the effects of QTLs outside the
tested region, that is, the genetic back-
ground. Genetic background effects are
assumed normally distributed: u ~ N(0, G*).
Note that G* represents the part of the
genetic (co)variance that is not explained
by the QTL. The extension from a single-
QTL model to a multi-QTL model is
straight­forward and given by
Q
y = Xβ + ∑ Xq QTL α q + Zu * +e.
q =1
Bilinear models with external covariables
When environmental (or genotypic) covari­
ables show high collinearity, interpretation
of the least squares regression coefficients
from the FR is complicated because they are
estimated very imprecisely. Noise on the
response variable also complicates the
interpretation of FR parameters.
Furthermore, least squares estimation of
parameters in FR models is not unique when
the number of covariables is larger than the
number of observations; therefore, an alter-
native estimation method is needed. Partial
least squares (PLS) regression can be used.
Multivariate PLS regression models
(Aastveit and Martens, 1986; Helland, 1988)
are a special class of bilinear models. When
genotypic responses over environments (Y)
are modelled using environmental covari­
ables, the J × H matrix Z of H (h = 1, 2, …, H)
environmental covariables can be written in
bilinear form as:
Z = t1p′1 + t2p′2 + … + tMp′M
  + EM = TP′ + E (14.7)
where the matrix T contains the t1…tJ J × 1
vectors called latent environmental covari­
ables or Z-scores (indexed by environments)
and the matrix P has the p1…pH H × 1 vectors
called Z-loadings (indexed by environmental
variables), and E has the residuals. Similarly,
the response variable matrix Y in bilinear
form is:
Y = t1q′1 + t2q′2 + … + tMq′M
  + FM = TQ′ + F (14.8)
where the matrix T is as in Eqn 14.7, the
matrix Q contains the q1…qI I × 1 vectors
called Y-loadings (indexed by genotypes),
and F has the residuals. The relationship
between Y and Z is transmitted through
latent variable T. The PLS algorithm
performs separate (but simultaneous) prin-
cipal component analysis of Z and of Y that
allows reducing the number of variables in
each system to a smaller number of hope-
fully more interpretable latent variables.
Treatment × environment interaction
analysis in an agronomy trial using PLS
A parsimonious description of the treatment
× environment interaction (T × E) occurring
in 24 agronomic treatments (tillage, summer
crop, manure and nitrogen, N) evaluated
during 10 consecutive years (1988–1997) was
conducted by Vargas et al. (2001) using FR
and PLS. Results of the final multiple FR
(MFR) analysis were compared with those of
PLS regression to achieve extra insight into
the T × E. The MFR was applied on the six
most important components of the T × E
terms: Year × Tillage, Year × Summer Crop,
Year × Manure, Year × N, Year × Summer Crop
× N, and Year × Manure × N. Results for the
MFR of the 27 environmental covariables ×
tillage interactions showed that evaporation
in December (EVD) × tillage sum of squares
accounted for 68% of the whole year × tillage
interaction. For year × summer crop, evap-
oration in April (EVA) accounted for 36% of
the year × summer crop. For year × manure,
precipitation in December (PRD) and sun
hours in February (SHF) contributed 56% of
the year × manure sum of squares. Year × N
interaction determined the major part of year
× treatment interaction sum of squares.
The PLS biplot separated the nine highest
yielding treatments (T9, T19, T21, T17, T11,
T12, T10, T23 and T18) from the nine lowest
yielding treatments (T1, T2, T3, T4, T5, T6,
T7, T8 and T16) (Fig. 14.3). The nine lowest
yielding treatments showed positive inter-
action with year 1995, which had high mTUF,
mTF and MTA (see Fig. 14.3 for explanation
of terms), but negative interaction with year
1988 (opposite quadrant). The PLS biplot
contains roughly five clusters of correlated
environmental covariables. The order of
276 J. Crossa et al.

Fig. 14.3.  Biplot of the first and second PLS (partial least squares) factors representing the Z-scores
(latent environmental covariable vectors) of 10 years (1988–1997), and the Y-loadings (response variable
vectors) of the 24 practice treatments (T1–T24) enriched with the Z-loadings (environmental variable
vectors) of 27 environmental variables. EV, total monthly evaporation; PR, total monthly precipitation; SH,
sun hours per day; mT, mean minimum temperature sheltered; MT, mean maximum temperature
sheltered; mTU, mean minimum temperature unsheltered; D, December; J, January; F, February; M,
March; A, April; N, nitrogen (adapted from Vargas et al., 2001).

inclusion of these covariables in the MFR
with the stepwise procedure for each factor
effect corresponds to selecting covariables
for the different cluster groups depicted in
Fig. 14.3.
Structural equation model (SEM)
The SEM approach is similar to multiple
regression that simultaneously analyses a
system of equations in which each equation
describes a causal relationship among vari-
ables considered in the system. The SEM
approach may be used to model intermedi-
ate traits (i.e. yield components) and their
interrelationships with other variables, as
well as with grain yield. Also, the SEM allows
a researcher to test hypotheses on cause–
effect relationships between variables in a
complex system. The initial definition of
SEM comprises a path diagram that reflects
the theoretical model and outlines the vari-
ous levels of observed (or latent) independ-
ent or dependent variables, as well as the
directions of causal relationships among
variables. The functional relationships
between variables are represented by arrows
or paths.
The SEM was proposed by Dhungana
(2004) to study GE of grain yield and its
components, and to account for the import-
ance of intermediate traits associated with
yield components. The author explained yield
GE with cross-products of genotypic and
environmental covariates as exogenous (inde-
pendent) variables and observed yield compo-
nent GE as endogenous (dependent/
independent) variables. The author con­­cluded
that SEM on observed variables was an effec-
tive way of describing yield GE in wheat, given
that the interrelationships and role of yield
 Statistical Models for GE Interaction 277

component GE can be incorporated simulta-
neously in a single model. Diagrams repre-
senting the structural model known as path
diagrams are useful for visualizing complex
models and variable relationships.
Vargas et al. (2007) showed how the SEM
method may be used on observed yield GE,
yield components GE, and other intermedi-
ate traits, together with residuals from
observed cross-product between genotypic
and environmental covariates, for studying
the causes and effects of GE on grain yield,
biomass, yield components, and other inter-
related variables acting at different develop-
ment stages in wheat trials. The proposed
model that formulates the hypotheses
between the endogenous variables associ-
ated with grain yield (YLDGE) and yield
components and the other variables (Y) at
different stages of crop development, and
the adjusted cross-products of genotypic and
environmental covariates (X) is given in Fig.
14.4. The given structural equation model
explained 0.96 of total variability of yield GE
(Table 14.6). The variables that contributed
most to explaining yield GE were GEs of yield
components GM2, TKW, GSP and SM2 (see
Table 14.6 for explanation of terms), with
total effects of 1.09, 0.64, 0.56 and 0.54,
respectively (Table 14.6 and Fig. 14.5). The
GEs of GM2, TKW, GSP and SPM explained
0.90, 0.43, 0.44 and 0.42, respectively, of
total variability. Yield component SM2 had a
very small R2 value (0.04), but a significant
indirect effect on grain yield GE (0.54). The
model indicated that GEs of yield compo-
nents GM2 and TKW had the largest positive
direct association with yield GE (1.09 and
0.64, respectively) and no indirect effects
(0.0), while GSP and SM2 GEs had the great-
est indirect effects on yield GE (0.61 and
0.54, respectively) and a low negative direct
effect (GSP = –0.05) or no direct effect at all
(SM2 = 0.0) on yield GE (Table 14.6).

β68
SM2

β12 β56
BMV dBMb
GM2
bij 2 β25
bij1 BMA β810
bij5
Xij β78
RSG
bij3
YLD
β34
GSP

β79
β47
SPM β910
bij4
TKW
bij 7
Xij

bij 9
Fig. 14.4.  Proposed model hypothesizing the relationship between yield GE (YLD) and yield components
GE, grains per square metre (GM2), thousand kernel weight (TKW), spikes per square metre (SM2),
grains per spike (GSP), biomass at anthesis (BMA), spike mass (SPM), relative duration of spike growth
(RSG), crop growth rate during spike growth (dBMb), biomass at the vegetative stage (BMV), and
adjusted cross-products (Xij) of the i th genotypic covariate and j th environmental covariate (i = 1, 2, …,
k; j = 1, 2, …, l ) . Arrows represent the direction of the variables’ influence. The βs and bs next to the
arrow lines represent the standardized coefficients to be estimated (e.g. bij1 is the coefficient for effect of
the cross-product of the ith genotypic covariate with the j th environmental covariate on yield (first
variable)) (adapted from Vargas et al., 2007).
278 J. Crossa et al.

Table 14.6.  Direct and indirect effects of yield components GE and adjusted cross-product covariates on
grain yield GE (R2 = 0.96) (adapted from Vargas et al., 2006).
Variable Direct effect Indirect effect Total effect R2
Grains per square metre (GM2) 1.09 0.00 1.09 0.90
Thousand kernel weight (TKW) 0.64 0.00 0.64 0.43
Grains per spike (GSP) –0.05 0.61 0.56 0.44
Spikes per square metre (SM2) 0.00 0.54 0.54 0.04
Spike mass (SPM) 0.00 –0.05 –0.05 0.42
Relative duration of spike growth (RSG) 0.00 0.09 0.09 –
Crop growth rate during spike growth (dBMb) 0.00 0.07 0.07 –
Biomass at anthesis (BMA) 0.00 –0.03 –0.03 –
Biomass at the vegetative stage (BMV) 0.00 –0.11 –0.11 –
MXT4 × GM2a 0.00 0.39 0.39 –
MXT4 × GSP 0.00 –0.23 –0.23 –
RAD2 × SM2 0.00 0.09 0.09 –
MNT4 × TKW 0.00 0.59 0.59 –
RAD2 × TKW 0.00 –0.40 –0.40 –
MXT3 × BMA 0.00 0.10 0.10 –
MNT1 × BMA 0.00 0.01 0.01 –
a MXT, mean daily maximum temperature; MNT, mean daily minimum temperature; RAD, solar radiation; suffixes 1, 2, 3

and 4 denote the first, second, third and fourth crop development stage, respectively.

Fig. 14.5.  Path estimates of the structural equation model for endogenous variables associated with
grains per square metre GE (GM2), grains per spike GE (GSP), thousand kernel weight GE (TKW), spikes
per square metre GE (SM2), relative duration of spike growth GE (RSG), crop growth rate during spike
growth GE (dBMb), biomass at anthesis GE (BMA), spike mass (SPM), biomass at the vegetative stage
GE (BMV), and yield GE (YLD), and cross-products (variables × environmental covariates). MXT, mean
daily maximum temperature; MNT, mean daily minimum temperature; RAD, solar radiation; suffixes 1, 2, 3
and 4 stand for the first, second, third and fourth crop development stages. Arrows represent the direction
of the variables’ influence, and the numbers on the arrow lines represent the estimated standardized
coefficients. Critical values for a significance level of 0.05, 0.01, 0.001 and 0.0001 are 2.00, 2.67, 3.48 and
4.20, respectively, using a two-tailed t-test with 60 degrees of freedom (adapted from Vargas et al., 2007).
 Statistical Models for GE Interaction 279
Searching for Associations Between
Molecular Markers and Phenotypic
Variability While Modelling Genotype
× Environment Interaction
The main feature of linear mixed model
methodology applied to plant phenotypic
data collected in METs is that it allows accu-
rate prediction of genotypic performance by
using covariance structures that consider
correlations between sites, years and plots
in the field, as well as genetic associations
between relatives. The genetic covariance
between relatives for any pair of related indi-
viduals (i and i′), due to their additive genetic
effects, is equal to two times the coefficient
of parentage (COP = fii′), also known as coef-
ficient of coancestry, times the additive
genetic variance (i.e. 2fii′ σ2a = A σ2a where A
is the additive relationship matrix and σ2a is
the additive genetic variance). Using the
linear mixed model methodology, the genetic
covariance matrix can be estimated and
BLUPs can be obtained. The effectiveness of
exploiting relationships among strains
tested in METs and the usefulness of these
BLUPs for simultaneously modelling the
main effects of genotypes and GE has been
studied by Crossa et al. (2006). The authors
obtained BLUPs of breeding values using
genetic variance-covariance structures
constructed as the Kroneker product (direct
product) of a structured matrix of genetic
variances and covariances across environ-
ments and a matrix of genetic relationships
between strains, A.
Usually association studies do not include
modelling GE simultaneously to the incorp-
oration of matrices Q (representing infor-
mation from population structure) and A
(denoting the additive relationship matrix).
Furthermore, COP information is rarely
incorporated in association mapping stud-
ies. We show how information on covariance
among relatives together with population
structure and GE can be used to search for
relationships between marker polymor-
phism and phenotypic variability.
Linear mixed model with covariance
between relatives and population
structure
This model is the same as that used by Crossa
et al. (2006) for fitting data from g geno-
types, s sites and r replicates (in each site),
assuming that the relationship of the geno-
types is measured by the g × g COP = fii′
matrix:
Y = X S b + ZR r + Z G g + e (14.9)
where X S is the design matrix of 0s and 1s
relating Y to the fixed effects of sites (b), and
ZR and ZG are the design matrices of 0s and
1s relating Y to the random effects of repli-
cates within sites (r) and genotypes within
sites (g), respectively. The random effect e
contains random effects of residuals within
sites. Vectors r, g and e are assumed to be
normally distributed with zero mean vectors
and variance-covariance matrices R, G and
E, respectively. The variance-covariance
matrix G combines the main effect of geno-
types and GE.
For each Diversity Array Technology
(DArT) marker, the BLUPs of the lines were
used to create the contrast for testing the
null hypothesis of no difference between the
BLUPs of the lines with the mth DArT marker
= 0 and the BLUPs of the lines with the mth
DArT marker = 1. This was done using the
variance-covariance matrix of the BLUPs of
the lines obtained from Eqn 14.9. An overall
test for the null hypothesis was developed
and used across all subpopulations obtained
from the population structure study.
Results
Results from application of this linear mixed
model to an analysis of DArT markers in
relation to disease traits in historical
CIMMYT wheat trials show that some mark-
ers were significantly associated with the
measured traits in chromosomal regions
where genes or QTLs have been previously
reported; also, significantly associated
Table 14.7.  Location of significant DArT markers (prefixed wPt) associated with leaf rust found in three historical CIMMYT Elite Spring Wheat Yield Trials

280
(ESWYT) for each chromosome and the reported Lr genes and QTLs (adapted from Crossa et al., 2007).a
Short arm (S) Long arm (L) Unknown arm
Chromosome DArT (wPt) Lr gene and QTL DArT (wPt) Lr gene and QTL DArT (wPt) Lr gene
1A 5374f, 2872, 4029, 6709 Lr10 8016, 0128 – – –
1B 1328, 3465, 4434, 0974, Lr26, QTL 0944, 2526, 4129 Lr46 2019, 5316, Lr33, Lr44, Lr55,
6427, 8986, 1781, 1139 Lr51
5065, 2614, 5678,
5363, 6777, 5801,
6117, 6833, 8616, 2315
1D – Lr21, QTL 3743 – – Lr40, Lr42, Lr43
2A 3114 Lr17a, Lr17b, Lr35, Lr45 – Lr38 6207 Lr11
2B 0100, 8326 Lr13, Lr16, Lr23, QTL 0049 Lr50 0094, 4559 Lr35
2D – Lr2a, Lr2b, Lr2c, Lr15, – Lr54 – –
Lr22a, Lr22b, Lr39,
Lr41, QTL
3A – – 1562, 9268, 1688 QTL – –

J. Crossa et al.
3B 0365, 7015, 7142, 5716, Lr27 – – – –
9310, 9170, 6047,
5105, 6802, 5769,
0384, 8096
3D 1336, 9401 – – Lr24 – Lr32
4A – – 4620 Lr28 5434, 7924 Lr25
4B 1272, 3908 Lr12, Lr31, QTL Lr30 – –
4D – – – QTL – –
5A 0605 – – 4249 –
5B – Lr52 3569, 4996, 5896, 3030, Lr18 4703 –
9598
5D 1400 – – Lr1 – –
6A 7475, 0864, 8006, 7938, – 4229 – – Lr56
9075
6B 3130, 4720, 3733 Lr36, Lr53 – Lr3a, Lr3bg, Lr3ka, – –
Lr9
7A 6034, 8789 Lr47 – Lr20 4553 –
7B – – 7887, 4300, 0600, 7108 Lr14a, Lr14b, QTL 9746 –
7D 1269, 3328 Lr29, Lr34 – Lr19 0934, 5150, –
  0366
a The location of Lr genes as per USDA-ARS-Cereal Disease Lab (http://www.ars.usda.gov/Main/docs.htm?docid=10342) and other publications. QTLs at these locations were reported
in other publications. The significant DArT markers and Lr genes with unknown location are given in the last two columns.
 Statistical Models for GE Interaction 281
markers­were found in regions where neither
genes nor QTLs have been reported for these
traits. Several of the known catalogued
genes, such as Lr47, were recently trans-
ferred from alien or related species and thus
not expected to be present in the material
included in this study.
Concerning disease traits, the variation of
pathogen races occurring at different loca-
tions is likely to reduce the identification of
race-specific resistance. Most of the known
catalogued genes are race-specific and effec-
tive only in some geographic areas. In this
study, disease pathogens may not have been
present at high frequencies in the years when
genotypes were evaluated in multiple loca-
tions. For example Lr3a (Table 14.7), which
occurs in several CIMMYT wheat lines, could
not be chosen in this study because virulence
to this gene is common worldwide. Virulence
to Lr1 is also common in most wheat grow-
ing areas, and the gene would have been diffi-
cult to detect even if more markers had
mapped to the chromosome containing Lr1.
Loss of effectiveness due to the presence of
virulent races is probably the reason why we
could not detect the chromosomal regions
for some genes known to be present in
CIMMYT wheat materials. Only a few genes,
such as Lr34/Yr18, Lr46/Yr29 and Yr30/Sr2,
are non-race specific in nature and should
have small-to-intermediate effects across
different environments. Analyses did, in fact,
identify chromosomal regions carrying the
above genes (Table 14.7).
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 Index
Page numbers in bold refer to figures and tables.
abiotic stresses 3
engineering solutions 3–4, 107, 108
heat 73, 74
inundation 98–100
low fertility (low-N) 132–133
salinity 95–96
anthropogenic, extent 93, 93
toxicity, mineral 72, 79, 93, 128, 188
water deficit 72–74, 73, 220
waterlogging 96–98
adaptation
agronomic strategies 77, 107–108, 255
assessment tools 117–118
autonomous 43–44
to combined stress factors 72, 108–109, 220
genetic traits 24, 77–78, 219–220
planned 44
aerobic rice 129–130, 189–190
aerosols 10, 16
agricultural pests and diseases 2–3, 25–28, 42
chemical control 65, 200–201
cultural control measures 64–65, 182,
205–212
dispersal 56–57, 63
epidemiology
disease triangle 51–52, 52
infection and colonization 53–56
latency 56
modelling and forecasting 65–66, 248,
255, 257
evolutionary forces 57, 58–59, 60
gene expression 61–62
geographical gene flow 61
interspecific hybridization 62
mutation and genetic drift 57
reproduction and diversity 62
survival rate, pathogen/pest 53
see also diseases; pests; soilborne diseases;
weeds
agricultural systems
choice of crops 64–65, 182
conservation agriculture 5, 170, 179–188
integrated management 63, 66, 107–108
low-input ideotypes 146–147, 263
monoculture or rotation 64, 169–170,
209–210, 211–212
sustainability 107, 170–171
workforce 39
allele mining 229
amphiploids 102–104, 220–221
anthesis–silking interval (ASI), maize 82, 272
aquaporins 78
backcrossing, marker-assisted 223
barley, climate response predictions 45, 45
biological control 27, 65, 201–202
biological nitrification inhibition (BNI) 165
biophysical interactions 24, 25
biotechnology 219, 221–223, 222, 237
see also genetic modification
285
286 Index

biotic stresses see agricultural pests and diseases; effects on soil properties 184–188, 185
weeds impact on GHG emissions
Brassica sp. seed meal, soil amendment carbon dioxide 188–189
206–208, 207, 208 methane 189–190
breeding see crop breeding nitrous oxide 190–192
principles 180
crop rotation 181
C3 and C4 crops ground cover and residue retention
introduction of C4 genes 78, 142, 145, 223 181–184, 183, 184
irrigation needs 74, 76 zero tillage 169, 181, 192
responses to CO2 levels 42, 139–140 range of applicability 180–181
canopy temperature (CT) Consultative Group on International
factors affecting 75, 250 Agricultural Research (CGIAR) 44
as root development indicator 81–82 consumption patterns, food
carbon capture see photosynthetic efficiency; related to wealth 39
sequestration, carbon urban and rural 39
carbon dioxide (CO2) cotton, climate response predictions 23
abundance and global warming potential Coupled Model Intercomparison Project (CMIP)
177–178, 178 12
acclimation 30, 74 cover crops 182
elevated levels 139 crop breeding
effect on disease susceptibility 62 for abiotic stress tolerance 3–4, 117–118
fertilizing effect 25, 28–30, 41, 41–42, 139 heat and drought 77, 78
interaction with heat and drought 74, salinity, waterlogging and inundation
76, 140 100, 101, 108–109
response modelling 250 cultivar design 78, 221–223
root/shoot partitioning 144 field testing
emissions projection 15, 15, 152 in disease hot spots 127
fixation 141–143 managed stress screening 130, 132–134
Cartagena Protocol on Biosafety (CBD) 236 multi-environment trials (METs)
cereals 117–118, 129, 264, 271
global production and trade 39, 46, 115–116 shuttle breeding 117–118, 131
response to warming 40, 120, 126, 126 statistical analysis see statistical models
temperate (wheat, barley) 72 germplasm resources 4, 84, 100–101, 102,
tropical (rice, sorghum, maize) 71 146
CIMMYT see International Maize and Wheat international collaboration 116–117,
Improvement Center 133–134, 232–233
cisgenics 228 pest and disease resistance 2–3, 63–64, 201
climate change selection performance indicators
20th century observations 10 canopy temperature 81–82
historical impacts 1 glaucousness 81
predictions 1–2, 10–11 grain yield 132
annual variability 42, 126 relative growth rate (RGR) 103
extreme events 20–21, 94 root porosity 97
rainfall patterns 19–20, 92, 94, 179 success prediction 135
sea level rise 21, 21–22, 92, 94 techniques 6, 79–80, 106–107, 220–221
temperature 18–19, 71 speed of delivery 219, 225, 234
rate of change 141 see also genetic modification; marker assisted
see also modelling, climate selection
conservation agriculture (CA) 5, 170 crop productivity
adoption encouragement 192–193 carbon dioxide enhancement effects 28–30,
economic benefits 179–180 41, 41–42, 139
 Index
empirical analysis 23
mechanistic crop modelling 23–24,
249–251
niche-based model approaches 24–25
predicted yield impacts 22–25, 44–45, 45
crops
choice of 64–65, 182
genetic diversity 220–221
induced 221
varieties
differences, modelling parameters
250–251, 265
geographical range 117, 271
older, useful traits in 143
wild relatives 79, 80, 101–104, 165, 220
priority geographical niches 248, 254
cultivable land, global 24
cuticular wax thickness 81
Decision Support System for Agrotechnology
Transfer (dssat) 23, 254
diseases
ecosystem introductions 61, 62
pre-emptive breeding 127
effects of microclimate 27–28
food safety impacts 28
fungal infection and humidity 53
pathogen species shifts 53, 56
responses to host stress 56, 78
spread 27, 56–57, 63
virulence 62
virus vectors 28, 53
see also soilborne diseases
Distichlis spp. (saltgrass) 104
drought
failed season models 248, 255
frequency and intensity 20, 179
impact on poor farmers 44
stress adaptations 72, 73, 220
economy, food
autonomous market responses 43
climate change impacts 38
global 45–47, 46
regional 47
consumption patterns 39, 115, 116
food prices 46
non-climatic trends 39–40
total food production 39, 115–116
trade 39, 46
use and limitations of economic models 46
287
edaphic factors see soils
El Niño-Southern Oscillation (ENSO) 10,
20–21, 42
emissions reduction measures
agricultural options, potential 152, 156,
188–192
agrochemical input reduction 145–146, 230
IPCC guidelines terminology 158
nitrification inhibitors 84, 146, 164–165
environments
characterization techniques 74, 131–133, 135
increasing variability of 263–264
marginal 78
target population of (TPE) 117, 129, 271
epidemics
climate change impacts 51, 57, 66
eruption conditions 51–52, 52
forecasting 65–66
Erosion Productivity Impact Calculator (epic)
23, 249, 255
erosion, soil 169, 180, 182
ethylene, heat stress signalling 78
evapotranspiration (ET) 40, 140
expressed sequence tag (EST) mapping 228,
229–230
extreme weather events 20–21, 94
factorial regression (FR) analysis 272–275
farmers
adaptation to climate change 38, 43–44
adoption of new practices 192–193
choice of crop varieties 129
‘Eh control’ water management 161–162
fertilizer efficiency savings 166–167
optimal land use assessment 108
fertilizers
application practices 163–164
management technologies
leaf colour charts 162
sensor-based 163, 166–167
nitrification inhibitor additives 164–165,
190–191
nitrogen inputs 144, 145–146, 162
organic amendments 206–208
P/K/N balance 165
slow/controlled release 164
flooding, coastal 22, 94
food security 22
geographical regions at risk 47, 128
global coordination 1, 116–117
improvement strategies 7–8
288 Index
fossil fuels, use in agriculture 167, 168, 188
Fourth Assessment Report (IPCC, 2007) 9, 11, 18,
42, 245
free-air CO2 enrichment (FACE) experiments
29–30, 30, 41, 41–42, 45
Fusarium head blight (FHB) 28, 53, 209
General Large Area Model (glam) 23, 24
genetic modification (GM) 4, 6
adoption needs and prospects 147–148,
230–231, 231
development pathways 233–235, 235
regulation 235–236, 236
technology access 232–233, 233, 236,
238
candidate genes 84–85, 104, 105–106, 227,
228–230
drought tolerance improvement 142
economic implications 231–232, 232,
233–234
herbicide resistance 145
root architecture and functions 146
rhizosphere disease suppression 212
Rubisco CO2 fixation 78, 141–142, 223
transformation techniques 226–228
genomic (genome-wide) selection (GS/GWS) 86,
134, 264
genomics research 221–222, 226
non-targeted mapping 229–230, 230
targeted mapping 228–229
genotype × environment (GE) interactions 7, 85
definition and causes 264
crossover interaction (COI) 269–271,
271
error in estimates 129
phenotype and molecular marker
associations 279–281, 280
trial data analysis 248
measurable values 265
see also statistical models
geographic information systems (GIS) 6–7, 131
coupling with crop simulation models
253–254
definition 246–247
integration with climate modelling data 246,
254, 255
range of uses 247, 247–249
global climate models (GCMs) 11–12, 13, 16
spatial resolution 16–17
government/international measures 43, 44
active stakeholder participation 193
agricultural research 116–117
GM technology development 231–232,
232, 234–236
early warning systems, disease outbreaks 66
tools for decision making 258
green manures 208–209
Green Revolution 1, 4, 44, 79
wheat breeding achievements 117–118
greenhouse gases (GHGs) 13, 139, 151–152
agriculture contribution 144–145, 151, 152,
177–180
effects of management practices 157,
160–170, 188–192
fossil fuel use 167, 168, 188
anthropogenic sources 177–179, 178
national inventories (NIGs) 158
groundnut, climate response predictions 23
halophytes, domestication 104, 108
harvest index (HI) 73, 77, 144
heat stress
adaptation traits 73
avoidance, rice flowering 84
evaporative cooling 74
managed stress screening, rice 130–131
physiological consequences 76–77
short-term heat exposure 42, 77, 140
herbicide tolerance 145, 181
selectable markers 227, 227
Hordeum marinum, trait selection 102–104, 103
humanitarian climate change impacts 39
food security 22, 47, 128
malnourishment 46, 46
hurricanes 20
hypoxia, waterlogged roots 96–97, 103
in vitro induced variation 221
infrastructure 39, 44
insertional mutagenesis 221
intellectual property and patents 232–233, 233
Intergovernmental Panel on Climate Change
(IPCC)
emissions scenario development 13–14
Fourth Assessment Report (FAR, 2007) 9, 11,
18, 42, 245
guidelines for emissions statistics 158, 158
Third Assessment Report (TAR, 2001) 9, 10
Working Group I (WGI) 10
International Maize and Wheat Improvement
Center (CIMMYT) 79–80, 117–118,
126–127, 133
 Index
International Rice Research Institute (IRRI) 79,
83, 130, 131
irrigation management guidelines 161–162
International Wheat Improvement Network
(IWIN) 118
Internet, use in epidemic forecasting 66
introgression techniques 84, 102, 104, 220
inundation
conservation agriculture benefits 184, 187,
187
physical stresses 98–99
tolerance and amelioration strategies
99–100, 130
ion toxicity 95, 95, 97
tolerance mechanisms 95–96
transgene candidates for tolerance 105
irrigation 42
brackish water, consequences 93–94
cost of expansion 44
management techniques 161–162
permanent raised beds 181, 186
water source reliability 128, 179
land use and land cover change (LULCC) 12
latency period, pests and diseases 56
livestock, global production and trade 39
fodder sources 104, 182
maize
anthesis–silking interval (ASI) 82, 272
breeding programmes for drought stress 82,
132–133
floret abortion in drought 77–78
genomic selection (GS) 134
global production 152, 154
mega-environment identification 131–132,
248
response predictions 23, 24, 44–45, 45
with simulation models 253, 253, 255
management practices 251
cropping systems 156, 169–170
fertilizer application 162–167
organic residue retention 168, 181–184,
183, 184
pest/disease control 64–65, 182, 205–209
tillage 165, 168–169, 181, 192–193
mapping, genetic 228–230
marker assisted selection (MAS) 3, 6, 79–80, 85
high throughput pheno/genotyping 225–226
marker systems 223, 224–225
289
recurrent (MARS) 86, 130, 264
screening support, conventional breeding
223–224, 233, 234
mechanistic crop modelling 23–24, 249–251
mega-environments (MEs) 4, 118, 120, 126,
135–136
maize, identification using GIS data
131–132, 248
rice, hydrological 128, 129
wheat, CIMMYT classification 118–126,
119, 121–125, 248
related to potential heat stress 254–255,
256
metabolite profiling 224
methane (CH4)
abundance and global warming potential
152, 178, 178
emissions from irrigated rice 144, 156,
158–160, 159, 189–190
microbial communities 168, 169, 182
analytical tools 213
introduction of biocontrol agents 202
model species 147, 222
modelling, climate 2
confidence level improvements 11
global circulation (GCMs) 11–12, 13, 16
GIS data compatibilty 246, 255
regional climate (RCMs) 16–18
Special Report Emissions Scenarios (SRES)
10, 12–15, 14, 255
uncertainty 10, 15–16, 107, 254
modelling, crop productivity see simulation
modelling; statistical models
monsoons 42
multi-location testing
advantages and disadvantages 117, 135–136
germplasm distribution networks 131,
133–134
trial data interpretation 132–133
using genomic selection 134
mutagenesis 221
National Center for Atmospheric Research
(NCAR) 19, 21
niche-based (agroecological zoning) approaches
24–25
nitrous oxide (N2O)
abundance and global warming potential
152, 178, 178–179
emissions from arable cropping 159, 160,
164
290 Index
nitrous oxide (N2O) continued
emissions from arable cropping continued
influence of tillage/residue regime
190–192
mid-season paddy-field drainage 161
nitrification inhibition 84, 146,
164–165
surplus inorganic nitrogen 162–164,
165–167
nutrients, mineral
cycling 162, 167, 190–191
deficiencies, micronutrient 72, 76
nitrogen use efficiency (NUE) 143–144, 144,
147
uptake efficiency 77
see also fertilizers
osmotic adjustment 96
ozone (O3) 42
partial least squares (PLS) regression analysis
275, 276
partitioning, root/shoot 144, 223, 250
pesticide use and toxicity 28, 65
pests
biological control 27, 65, 201–202
distribution and abundance 26
integrated pest management (IPM) 65, 66,
182
phytosanitary precautions 63
resistance, molecular markers 80
winter survival 26, 53
phenology and stress avoidance 77, 99, 251
phenotyping 86
high-throughput technologies 225–226
marker-assisted recurrent selection (MARS)
86
and predictive plant modelling 222
photorespiration 76, 77, 140, 142
photosynthetic efficiency
carbon metabolism factors 141–142
at high temperatures 140, 143
related to nitrogen uptake 143–144
simulation model parameters 249–250
sink plasticity 143, 223
under water stress 142
phytoremediation 212
population growth 39
potato late blight 56, 62, 65
probability distribution function (pdf) 44
productivity see crop productivity
promoters (DNA transcription) 227–228
quantitative trait loci (QTL)
colinearity, evolutionary 229
drought and heat adaptations 78, 83, 85–86
environmental covariables 272–276, 276
genome-wide selection (GWS) 86
identification of key genes 146, 225, 228
multitrait multi-environment analysis
273–275
pyramiding multiple traits 224
radial oxygen loss (ROL) barriers 97–98
radiation use efficiency (RUE) 73, 250
rainfall patterns
buffering by conservation agriculture 184,
186, 186–187, 187
failed season modelling 248, 255
predicted changes 19–20, 40–41, 92, 94
regional climate models (RCMs) 16–18
rice
climate change response predictions 23, 40,
41, 255, 257
irrigated and rainfed crops 128–129
flowering, drought stress responses 83–84
global production 152, 153
comparison of flooded and aerobic 190
flooding management regimes 129, 152,
158, 161–162
hydrological mega-environments 128, 129
inundation tolerance 99–100, 102, 130
methane emission from rice fields 144, 156,
158–161, 159, 189–190
root growth, near-isogenic lines (NILs) 83
roots
biological nitrification inhibition (BNI) 165
exudates 209
interactions with rhizobacteria 205
nutrient uptake optimization, transgenic 146
porosity (aerenchyma) 97, 98, 99
radial oxygen loss (ROL) barriers 97–98
role in heat/drought stress mitigation 77
rotation, crop 169–170, 181, 209–210
Rubisco enzyme activity 78, 141–142, 223
salinity
increase, with sea level rise 22, 94
physiological tolerance 95–96
 Index
primary and secondary causes 93
toxic effects 95, 95, 97
saltbushes (Atriplex spp.), as fodder 104
sea level rise 21, 21–22, 92, 94
seasonal forecasting 17–18
senescence delay, sorghum 83
sequestration, carbon 152, 167–170, 188–189
shuttle breeding 117–118, 131
simulation modelling 6–7, 74, 224
accuracy and data availability 257
data inputs required 249, 249–251
named examples in use 246, 249
operation 251–253, 252, 253
use of GIS data 253–254
smallholder/subsistence farming 22, 47, 255
sodicity 93, 188
soilborne diseases 5–6, 56
control alternatives 200–202, 201, 211
naturally suppressive soils 202–203
effect of green manures 208–209
examples showing disease decline
203–204
functional microbial populations
204–205
influence of crop cultivar genotype
210–211
responses to organic amendments
205–208, 207, 208
prevalence and yield losses 200
responses to crop rotation 209–210,
211–212
soils
erosion 169, 180, 182
microbial community 168, 169, 182,
202–204
moisture level, crop responses 40–41,
189–190
organic carbon (SOC) pool 167–170
porosity 187–188
temperature 188
water-holding capacity 72, 182, 184
sorghum
crop importance and uses 82–83
stay-green drought breeding 82–83
soybean
planting date modelling 251–253, 252
response predictions 23
Special Report Emissions Scenarios (SRES) 10,
12–15, 14, 255
starch synthase, soluble 78, 85
statistical models
factorial regression (FR) 272–275
291
linear two-way fixed-effect 265–266, 267
linear–bilinear 269–271
fixed-effect 266, 268, 268
mixed-effect 268–269
partial least squares (PLS) 275, 276
structural equation (SEM) 272, 276–277
sterility, caused by heat/drought stress 77, 78,
83–84
suppressive soils see soilborne diseases
sustainable technologies 4–6, 170–171, 192–193
temperature changes
canopy temperature (CT) 75, 78, 81–82
critical maximum, for pollination 140
crop growth
optima 74, 246
radiation use efficiency (RUE) 73, 250
responses to increased warmth 40, 77,
140, 143
effect on disease resistance genes 61, 201
effects on seawater/ice 21, 92
pathogen/pest survival 53
predicted rate and extent 18–19
Third Assessment Report (IPCC, 2001) 9, 10
tillage 4, 5
alternative weed control measures 181
effects on GHG emissions 165, 168–169,
188–192
intensive, long-term effects 180
stubble-borne disease risk 65
transcript profiling 222
transformation, genetic 226–228
transgenic technologies see genetic modification
(GM)
transpiration efficiency 77, 78
impact on nitrogen uptake 144
uncertainty
climate projections 10, 15–16, 107, 254
temperature sensitivity, crop 40
urbanization, effect on consumption patterns
39
vegetative index, crop canopy 163
warming, global
potential (GWP) of gases 152
predictions 18–19
292 Index
water supplies 42, 72
management in rice cultivation 161–162
quality, and water table depth 93, 94
see also irrigation
water use efficiency (WUE) 62, 72, 79, 81, 144
waterlogging
root-zone hypoxia 96–97, 103
tolerance mechanisms 97–98
weeds 181, 190
wheat
amphiploidy, with wild grasses 102–104,
220–221
breeding for wide geographical range
117–118, 126–128
climate change response predictions 23, 24,
45, 45, 120
drought adaptation breeding approaches
79–80, 127–128
Australian breeding programme 79
hot, dry environments 80–81
fungal diseases 53, 56, 63, 64, 203
global production 152, 155
hot, irrigated environments 81
mega-environments 118–126, 119,
121–125, 179
model prediction of heat/drought stress
254–255, 256
root characteristics 81
salt-tolerant cultivars 102
Yaqui Valley case study 163, 165–167
wide crossing techniques 79–80, 84
Yaqui Valley spring wheat case study 163,
165–167
yield
impacts of climate change 22–25, 44–45, 45
temperature increase and cereals 120,
126, 126
improvement through breeding 79, 80
component traits 142–143, 277–278,
278
heritability (H), broad-sense 132
trial SEM analysis 276–277, 277
optimization potential 145, 223
stability 126–127, 143, 264